Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 17:07:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/04_2023/6mdn_9101_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/04_2023/6mdn_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_9101/04_2023/6mdn_9101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/04_2023/6mdn_9101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/04_2023/6mdn_9101_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/04_2023/6mdn_9101_trim_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 388": not complete - not flipped Residue "A ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 617": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 413": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B LEU 420": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "B ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 691": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C LEU 484": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "C ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 446": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 725": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 727": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 22.57, per 1000 atoms: 0.31 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 48.55 Conformation dependent library (CDL) restraints added in 5.0 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... running ksdssp... Secondary structure from input PDB file: 186 helices and 35 sheets defined 44.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 242 through 248 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 267 through 276 removed outlier: 3.739A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 295 through 316 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 351 through 358 Processing helix chain 'A' and resid 400 through 417 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 426 through 431 removed outlier: 3.805A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 455 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 482 through 487 removed outlier: 5.001A pdb=" N ASP A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 512 through 529 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 549 through 558 Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.634A pdb=" N LYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.862A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.949A pdb=" N GLU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.788A pdb=" N ILE A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.886A pdb=" N GLU A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 114 through 124 Processing helix chain 'B' and resid 224 through 239 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 242 through 248 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 297 through 315 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 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 381 through 384 No H-bonds generated for 'chain 'B' and resid 381 through 384' Processing helix chain 'B' and resid 400 through 416 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) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 438 through 456 removed outlier: 3.972A pdb=" N GLU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 512 through 529 Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 578 through 594 removed outlier: 3.552A pdb=" N ALA B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.953A pdb=" N LYS B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 707 through 718 removed outlier: 3.932A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 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 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 87 through 90 No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.549A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 297 through 308 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) removed outlier: 4.697A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 348 through 358 removed outlier: 3.554A pdb=" N SER C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 381 through 384 No H-bonds generated for 'chain 'C' and resid 381 through 384' Processing helix chain 'C' and resid 400 through 410 removed outlier: 3.545A pdb=" N LEU C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 439 through 456 Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 498 through 502 removed outlier: 3.736A pdb=" N TYR C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 502' Processing helix chain 'C' and resid 512 through 530 Processing helix chain 'C' and resid 550 through 560 removed outlier: 3.635A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 594 removed outlier: 3.622A pdb=" N LYS C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 620 through 630 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 688 through 698 removed outlier: 4.061A pdb=" N THR C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 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 725 through 737 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 14 through 18 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 236 through 239 No H-bonds generated for 'chain 'D' and resid 236 through 239' Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 266 through 275 removed outlier: 4.865A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 315 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 346 through 358 removed outlier: 3.937A pdb=" N VAL D 351 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 355 " --> pdb=" O ASN D 352 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 416 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 426 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 439 through 457 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 482 through 488 Processing helix chain 'D' and resid 512 through 530 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 549 through 560 removed outlier: 3.705A pdb=" N ALA D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 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 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 621 through 631 removed outlier: 3.901A pdb=" N LYS D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 652 through 655 No H-bonds generated for 'chain 'D' and resid 652 through 655' Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 688 through 695 Processing helix chain 'D' and resid 707 through 719 removed outlier: 4.263A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 736 removed outlier: 3.982A pdb=" N VAL D 726 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 736 " --> pdb=" O LEU D 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 114 through 122 removed outlier: 3.926A pdb=" N ILE E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 266 through 277 Processing helix chain 'E' and resid 297 through 316 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 330 through 333 No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 380 through 383 No H-bonds generated for 'chain 'E' and resid 380 through 383' Processing helix chain 'E' and resid 400 through 410 Processing helix chain 'E' and resid 412 through 415 No H-bonds generated for 'chain 'E' and resid 412 through 415' Processing helix chain 'E' and resid 426 through 432 removed outlier: 4.521A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 454 removed outlier: 3.889A pdb=" N ALA E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 512 through 530 Processing helix chain 'E' and resid 549 through 560 Processing helix chain 'E' and resid 570 through 573 Processing helix chain 'E' and resid 578 through 583 Processing helix chain 'E' and resid 585 through 593 Processing helix chain 'E' and resid 605 through 609 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.834A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 655 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 688 through 697 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) Processing helix chain 'E' and resid 707 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 726 through 735 removed outlier: 4.179A pdb=" N ALA E 731 " --> pdb=" O ARG E 727 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 735 " --> pdb=" O ALA E 731 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 238 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 266 through 277 removed outlier: 3.588A pdb=" N GLY F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 315 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 359 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 400 through 410 Processing helix chain 'F' and resid 428 through 431 No H-bonds generated for 'chain 'F' and resid 428 through 431' Processing helix chain 'F' and resid 433 through 435 No H-bonds generated for 'chain 'F' and resid 433 through 435' Processing helix chain 'F' and resid 444 through 447 No H-bonds generated for 'chain 'F' and resid 444 through 447' Processing helix chain 'F' and resid 450 through 453 No H-bonds generated for 'chain 'F' and resid 450 through 453' Processing helix chain 'F' and resid 499 through 502 No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 512 through 529 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) Processing helix chain 'F' and resid 550 through 559 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 578 through 594 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 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 620 through 631 removed outlier: 3.627A pdb=" N LYS F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 655 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 688 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 707 through 719 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 725 through 735 Processing helix chain 'H' and resid 20 through 34 removed outlier: 3.575A pdb=" N SER H 25 " --> pdb=" O ALA H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 82 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 201 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) Processing helix chain 'I' and resid 193 through 236 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 239 through 254 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) Processing helix chain 'J' and resid 32 through 67 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) Processing helix chain 'J' and resid 69 through 85 removed outlier: 3.754A pdb=" N GLY J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 16 Processing helix chain 'K' and resid 37 through 55 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) removed outlier: 3.974A pdb=" N ALA K 55 " --> pdb=" O MET K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 74 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) Processing helix chain 'K' and resid 81 through 94 removed outlier: 4.085A pdb=" N PHE K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 114 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 118 through 133 removed outlier: 3.800A pdb=" N SER K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 155 removed outlier: 4.425A pdb=" N ALA K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 175 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 179 through 194 removed outlier: 3.931A pdb=" N ASP K 194 " --> pdb=" O THR K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 211 Processing helix chain 'K' and resid 220 through 227 Processing helix chain 'K' and resid 235 through 238 Processing helix chain 'K' and resid 242 through 252 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 256 through 269 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 274 through 291 Processing helix chain 'L' and resid 10 through 20 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 37 through 54 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 60 through 70 removed outlier: 3.725A pdb=" N ALA L 69 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 94 removed outlier: 3.694A pdb=" N LYS L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 111 removed outlier: 3.899A pdb=" N ILE L 110 " --> pdb=" O ARG L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 133 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 138 through 154 removed outlier: 3.565A pdb=" N GLN L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 170 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 185 through 193 removed outlier: 3.721A pdb=" N GLY L 189 " --> pdb=" O TYR L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 211 removed outlier: 4.687A pdb=" N LYS L 203 " --> pdb=" O TYR L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 227 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 241 through 251 Processing helix chain 'L' and resid 257 through 267 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 274 through 291 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) Processing sheet with id= A, first strand: chain 'A' and resid 392 through 395 removed outlier: 9.320A pdb=" N MET A 393 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 257 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 395 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR A 259 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 256 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY A 260 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR A 373 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS A 323 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 370 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 283 " --> pdb=" O ILE A 326 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 663 through 666 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) removed outlier: 6.675A pdb=" N LEU A 640 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL A 539 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE A 642 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU A 541 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 644 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 566 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= D, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.069A pdb=" N VAL B 60 " --> pdb=" O ALA B 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 22 through 24 Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.667A pdb=" N GLU B 153 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B 95 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 151 " --> pdb=" O MET B 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= I, first strand: chain 'B' and resid 135 through 140 Processing sheet with id= J, first strand: chain 'B' and resid 369 through 373 removed outlier: 3.562A pdb=" N THR B 373 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 260 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 283 through 285 Processing sheet with id= L, first strand: chain 'B' and resid 663 through 666 removed outlier: 8.705A pdb=" N VAL B 539 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 642 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 541 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY B 644 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 566 " --> pdb=" O CYS B 599 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.554A pdb=" N ALA C 81 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.467A pdb=" N VAL C 60 " --> pdb=" O ALA C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 182 through 187 removed outlier: 5.612A pdb=" N GLU C 98 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL C 149 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP C 100 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU C 147 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 131 Processing sheet with id= Q, first strand: chain 'C' and resid 391 through 395 removed outlier: 6.803A pdb=" N GLY C 371 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY C 260 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR C 373 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 323 through 326 removed outlier: 3.654A pdb=" N LEU C 368 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 663 through 667 removed outlier: 6.630A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU C 541 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY C 644 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY C 543 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR C 646 " --> pdb=" O GLY C 543 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 4 through 7 removed outlier: 12.652A pdb=" N GLU D 77 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N SER D 40 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 24 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.242A pdb=" N VAL D 60 " --> pdb=" O ALA D 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 182 through 187 Processing sheet with id= W, first strand: chain 'D' and resid 129 through 131 Processing sheet with id= X, first strand: chain 'D' and resid 170 through 172 removed outlier: 4.346A pdb=" N GLN D 170 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE D 152 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP D 151 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 392 through 394 removed outlier: 9.045A pdb=" N MET D 393 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 257 " --> pdb=" O MET D 393 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL D 369 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU D 258 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY D 371 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 663 through 667 removed outlier: 6.562A pdb=" N LEU D 640 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL D 539 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY D 543 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR D 646 " --> pdb=" O GLY D 543 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= AB, first strand: chain 'E' and resid 8 through 10 removed outlier: 6.530A pdb=" N VAL E 60 " --> pdb=" O ALA E 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 182 through 187 Processing sheet with id= AD, first strand: chain 'E' and resid 128 through 131 Processing sheet with id= AE, 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: 6.790A pdb=" N LEU E 368 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE E 327 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE E 370 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 540 through 542 removed outlier: 7.981A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 603 " --> pdb=" O CYS E 568 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 92 through 96 removed outlier: 7.099A pdb=" N GLU E 153 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET E 95 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP E 151 " --> pdb=" O MET E 95 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 283 through 286 removed outlier: 6.761A pdb=" N ILE F 324 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASN F 286 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 326 " --> pdb=" O ASN F 286 " (cutoff:3.500A) 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= AI, first strand: chain 'F' and resid 536 through 542 removed outlier: 6.846A pdb=" N LEU F 640 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU F 541 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY F 644 " --> pdb=" O LEU F 541 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 600 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR F 645 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL F 602 " --> pdb=" O THR F 645 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI 1307 hydrogen bonds defined for protein. 3756 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: 27.44 Time building geometry restraints manager: 51.10 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: 78.06 - 89.92: 28 89.92 - 101.79: 189 101.79 - 113.65: 90116 113.65 - 125.52: 41457 125.52 - 137.39: 1445 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: 28748 35.92 - 71.84: 187 71.84 - 107.76: 16 107.76 - 143.68: 5 143.68 - 179.60: 2 Dihedral angle restraints: 28958 sinusoidal: 14029 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 28955 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: 385 1.90 - 2.58: 84197 2.58 - 3.25: 221795 3.25 - 3.93: 272749 3.93 - 4.60: 431056 Nonbonded interactions: 1010182 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=" O GLU F 297 " pdb=" H ASN F 301 " model vdw 1.519 1.850 nonbonded pdb=" O LEU K 219 " pdb=" H LEU K 223 " model vdw 1.543 1.850 ... (remaining 1010177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.810 Extract box with map and model: 7.670 Check model and map are aligned: 0.820 Set scattering table: 0.480 Process input model: 175.250 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.690 ------------------------------------------------------------------------------- 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= 1.050 Angle : 1.673 29.023 49842 Z= 1.011 Chirality : 0.116 2.978 5651 Planarity : 0.009 0.076 6415 Dihedral : 11.657 179.603 14002 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 % 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 *********************** 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 : 4.563 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 outliers start: 15 outliers final: 7 residues processed: 291 average time/residue: 1.0191 time to fit residues: 462.7322 Evaluate side-chains 223 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 4.469 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.7520 time to fit residues: 14.6959 ------------------------------------------------------------------------------- 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: 30.0000 chunk 192 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 358 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 266 optimal weight: 50.0000 chunk 415 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 ASN A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 272 GLN C 374 ASN C 435 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 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 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 GLN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN D 697 GLN D 719 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN E 495 ASN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 ASN F 675 GLN H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 HIS K 123 HIS ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 36963 Z= 0.218 Angle : 0.686 11.387 49842 Z= 0.367 Chirality : 0.062 1.682 5651 Planarity : 0.005 0.066 6415 Dihedral : 8.932 179.794 4963 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.80 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.78 (0.11), residues: 4570 helix: -1.76 (0.10), residues: 2040 sheet: -1.64 (0.18), residues: 614 loop : -1.83 (0.13), residues: 1916 *********************** 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 266 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 260 time to evaluate : 4.571 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 outliers start: 6 outliers final: 3 residues processed: 265 average time/residue: 1.0268 time to fit residues: 429.6374 Evaluate side-chains 228 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6771 time to fit residues: 9.4245 ------------------------------------------------------------------------------- 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: 7.9990 chunk 128 optimal weight: 50.0000 chunk 345 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 415 optimal weight: 9.9990 chunk 449 optimal weight: 0.9980 chunk 370 optimal weight: 9.9990 chunk 412 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 333 optimal weight: 5.9990 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 36963 Z= 0.238 Angle : 0.621 10.936 49842 Z= 0.340 Chirality : 0.061 1.699 5651 Planarity : 0.004 0.050 6415 Dihedral : 8.162 178.818 4963 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.75 % Rotamer Outliers : 0.05 % 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: -2.17 (0.11), residues: 4570 helix: -1.16 (0.10), residues: 2036 sheet: -1.34 (0.18), residues: 597 loop : -1.62 (0.13), residues: 1937 *********************** 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 : 4.465 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 outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.9942 time to fit residues: 387.0550 Evaluate side-chains 222 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 4.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5553 ------------------------------------------------------------------------------- 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: 9.9990 chunk 312 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 198 optimal weight: 30.0000 chunk 279 optimal weight: 50.0000 chunk 417 optimal weight: 20.0000 chunk 441 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 395 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 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 272 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 669 ASN ** E 20 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 254 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 36963 Z= 0.238 Angle : 0.604 10.877 49842 Z= 0.327 Chirality : 0.061 1.688 5651 Planarity : 0.004 0.110 6415 Dihedral : 7.879 178.947 4963 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 4570 helix: -0.92 (0.11), residues: 2063 sheet: -1.29 (0.19), residues: 609 loop : -1.57 (0.13), residues: 1898 *********************** 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 234 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 4.727 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 outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 1.0397 time to fit residues: 390.0078 Evaluate side-chains 213 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 4.573 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8460 ------------------------------------------------------------------------------- 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: 10.0000 chunk 6 optimal weight: 4.9990 chunk 328 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 376 optimal weight: 30.0000 chunk 305 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 chunk 111 optimal weight: 0.2980 overall best weight: 5.6588 ------------------------------------------------------------------------------- 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 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4078 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= 0.223 Angle : 0.575 10.914 49842 Z= 0.311 Chirality : 0.061 1.697 5651 Planarity : 0.004 0.050 6415 Dihedral : 7.623 179.789 4963 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.65 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4570 helix: -0.77 (0.11), residues: 2082 sheet: -1.21 (0.19), residues: 609 loop : -1.55 (0.14), residues: 1879 *********************** 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 235 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 4.549 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 outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 1.0611 time to fit residues: 400.3433 Evaluate side-chains 211 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 4.505 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7706 ------------------------------------------------------------------------------- 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: 6.9990 chunk 397 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 259 optimal weight: 0.3980 chunk 109 optimal weight: 5.9990 chunk 442 optimal weight: 20.0000 chunk 367 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- 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 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 669 ASN E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** L 274 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 36963 Z= 0.205 Angle : 0.558 11.108 49842 Z= 0.299 Chirality : 0.061 1.699 5651 Planarity : 0.004 0.076 6415 Dihedral : 7.334 179.298 4963 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.24 % Favored : 93.74 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 4570 helix: -0.61 (0.11), residues: 2092 sheet: -1.17 (0.19), residues: 614 loop : -1.50 (0.14), residues: 1864 *********************** 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 228 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 4.899 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 outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 1.0214 time to fit residues: 372.1991 Evaluate side-chains 213 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 4.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7390 ------------------------------------------------------------------------------- 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: 8.9990 chunk 49 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 372 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 440 optimal weight: 3.9990 chunk 275 optimal weight: 50.0000 chunk 268 optimal weight: 7.9990 chunk 203 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 418 GLN ** 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 505 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7562 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 36963 Z= 0.203 Angle : 0.554 10.946 49842 Z= 0.297 Chirality : 0.061 1.702 5651 Planarity : 0.004 0.063 6415 Dihedral : 7.199 179.535 4963 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.63 % Favored : 93.35 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4570 helix: -0.45 (0.11), residues: 2082 sheet: -1.13 (0.19), residues: 606 loop : -1.48 (0.14), residues: 1882 *********************** 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 226 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 4.565 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 outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 1.0197 time to fit residues: 367.9969 Evaluate side-chains 207 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 4.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6387 ------------------------------------------------------------------------------- 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: 30.0000 chunk 175 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 132 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 280 optimal weight: 50.0000 chunk 300 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 410 HIS ** 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 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 505 ASN D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 GLN ** 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: 0.7619 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 36963 Z= 0.249 Angle : 0.586 10.932 49842 Z= 0.318 Chirality : 0.061 1.715 5651 Planarity : 0.004 0.053 6415 Dihedral : 7.252 179.763 4963 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.24 % Favored : 92.74 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4570 helix: -0.54 (0.11), residues: 2097 sheet: -1.19 (0.19), residues: 607 loop : -1.50 (0.14), residues: 1866 *********************** 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 : 5.159 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 outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 1.0288 time to fit residues: 368.8353 Evaluate side-chains 203 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6941 ------------------------------------------------------------------------------- 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: 10.0000 chunk 421 optimal weight: 20.0000 chunk 385 optimal weight: 0.9990 chunk 410 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 125 optimal weight: 50.0000 chunk 370 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 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 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** 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 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 36963 Z= 0.216 Angle : 0.567 10.966 49842 Z= 0.304 Chirality : 0.061 1.715 5651 Planarity : 0.004 0.054 6415 Dihedral : 7.158 179.411 4963 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.07 % Favored : 92.91 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4570 helix: -0.46 (0.11), residues: 2102 sheet: -1.15 (0.20), residues: 609 loop : -1.41 (0.14), residues: 1859 *********************** 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 222 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.9893 time to fit residues: 354.1214 Evaluate side-chains 207 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 4.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6384 ------------------------------------------------------------------------------- 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: 50.0000 chunk 434 optimal weight: 30.0000 chunk 264 optimal weight: 50.0000 chunk 205 optimal weight: 10.0000 chunk 301 optimal weight: 0.3980 chunk 455 optimal weight: 2.9990 chunk 419 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 280 optimal weight: 50.0000 chunk 222 optimal weight: 10.0000 overall best weight: 5.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 36963 Z= 0.226 Angle : 0.570 10.961 49842 Z= 0.307 Chirality : 0.061 1.710 5651 Planarity : 0.004 0.054 6415 Dihedral : 7.105 179.043 4963 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.59 % Favored : 92.39 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4570 helix: -0.46 (0.11), residues: 2111 sheet: -1.16 (0.20), residues: 609 loop : -1.40 (0.14), residues: 1850 ********************** 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 224 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 4.562 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 outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 1.0012 time to fit residues: 362.1524 Evaluate side-chains 205 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5975 ------------------------------------------------------------------------------- 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: 4.9990 chunk 111 optimal weight: 8.9990 chunk 334 optimal weight: 0.2980 chunk 53 optimal weight: 30.0000 chunk 100 optimal weight: 0.9990 chunk 363 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 372 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** 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 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** F 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.042410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.030858 restraints weight = 1727256.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.031778 restraints weight = 653917.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.032452 restraints weight = 332120.148| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 36963 Z= 0.145 Angle : 0.536 11.025 49842 Z= 0.277 Chirality : 0.062 1.706 5651 Planarity : 0.003 0.053 6415 Dihedral : 6.891 178.678 4963 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.71 % Favored : 94.27 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4570 helix: -0.03 (0.11), residues: 2101 sheet: -0.95 (0.20), residues: 605 loop : -1.21 (0.14), residues: 1864 =============================================================================== Job complete usr+sys time: 9587.03 seconds wall clock time: 169 minutes 38.47 seconds (10178.47 seconds total)