Starting phenix.real_space_refine (version: dev) on Wed Dec 14 21:30:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/12_2022/6mdm_9100_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/12_2022/6mdm_9100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/12_2022/6mdm_9100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/12_2022/6mdm_9100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/12_2022/6mdm_9100_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/12_2022/6mdm_9100_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 Convert atoms to be neutral 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 TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 413": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 238": "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 PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 725": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 727": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 73171 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11004 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 29, 'TRANS': 669} Chain breaks: 3 Chain: "B" Number of atoms: 11079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 11079 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 29, 'TRANS': 674} Chain breaks: 3 Chain: "C" Number of atoms: 11164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 11164 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 29, 'TRANS': 679} Chain breaks: 3 Chain: "D" Number of atoms: 11232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 11232 Classifications: {'peptide': 713} Link IDs: {'PTRANS': 29, 'TRANS': 683} Chain breaks: 3 Chain: "E" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8130 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 21, 'TRANS': 492} Chain breaks: 2 Chain: "F" Number of atoms: 7007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7007 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 5 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "H" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2301 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1060 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "J" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 984 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4430 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 3, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4447 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 3, 'TRANS': 282} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.75, per 1000 atoms: 0.35 Number of scatterers: 73171 At special positions: 0 Unit cell: (149.34, 148.03, 221.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 210 16.00 P 31 15.00 O 7008 8.00 N 6342 7.00 C 22976 6.00 H 36604 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 50.77 Conformation dependent library (CDL) restraints added in 5.6 seconds 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 36 sheets defined 43.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 14 through 17 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.607A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.347A pdb=" N GLN A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.619A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 removed outlier: 4.474A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 400 through 417 removed outlier: 4.454A pdb=" N ARG A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 4.160A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 455 removed outlier: 4.018A pdb=" N GLU A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 485 No H-bonds generated for 'chain 'A' and resid 482 through 485' 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: 3.895A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 4.354A pdb=" N SER A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 578 through 594 removed outlier: 3.819A pdb=" N CYS A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 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: 3.805A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.732A pdb=" N GLU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.710A 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 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 114 through 124 Processing helix chain 'B' and resid 224 through 239 removed outlier: 5.626A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 297 through 315 removed outlier: 4.446A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 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 415 removed outlier: 3.652A pdb=" N LEU B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 440 through 455 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 removed outlier: 3.527A pdb=" N LEU B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 578 through 594 removed outlier: 3.688A pdb=" N ALA B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 4.030A 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: 3.873A 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 removed outlier: 3.541A pdb=" N ALA B 679 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 697 Processing helix chain 'B' and resid 707 through 718 removed outlier: 4.186A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.366A pdb=" N VAL B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 64 through 70 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 122 removed outlier: 3.815A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' 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 275 Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.805A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 349 through 358 removed outlier: 3.666A 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 416 removed outlier: 3.906A pdb=" N GLN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 439 through 456 removed outlier: 3.833A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 497 through 502 removed outlier: 3.809A pdb=" N SER C 501 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 530 Processing helix chain 'C' and resid 550 through 560 removed outlier: 3.572A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 594 removed outlier: 3.792A 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 691 through 698 Processing helix chain 'C' and resid 707 through 718 removed outlier: 4.112A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 737 removed outlier: 4.373A pdb=" N GLU C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 18 removed outlier: 3.519A pdb=" N LEU D 18 " --> pdb=" O GLU D 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 18' Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 114 through 121 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 243 through 247 Processing helix chain 'D' and resid 266 through 275 removed outlier: 5.342A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 315 removed outlier: 4.087A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 358 removed outlier: 3.778A pdb=" N VAL D 350 " --> pdb=" O HIS D 347 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 351 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 355 " --> pdb=" O ASN D 352 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 358 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.928A pdb=" N HIS D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.241A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 488 Processing helix chain 'D' and resid 512 through 530 removed outlier: 4.204A pdb=" N GLN D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 578 through 593 removed outlier: 3.992A pdb=" N MET D 585 " --> pdb=" O LYS D 581 " (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: 4.026A 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 698 removed outlier: 5.301A pdb=" N GLN D 697 " --> pdb=" O THR D 693 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 698 " --> pdb=" O ILE D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 718 removed outlier: 4.138A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 736 removed outlier: 3.845A pdb=" N GLU D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' 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: 4.052A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 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 415 removed outlier: 4.253A pdb=" N ARG E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 removed outlier: 4.312A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 454 removed outlier: 3.536A pdb=" N GLN E 449 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 488 removed outlier: 3.961A pdb=" N ILE E 488 " --> pdb=" O LEU E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 530 Processing helix chain 'E' and resid 550 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 594 Processing helix chain 'E' and resid 605 through 609 Processing helix chain 'E' and resid 620 through 630 removed outlier: 5.085A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 654 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 688 through 697 removed outlier: 3.673A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 718 removed outlier: 3.733A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 735 removed outlier: 4.006A pdb=" N ALA E 731 " --> pdb=" O ARG E 727 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU E 735 " --> pdb=" O ALA E 731 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 238 removed outlier: 3.520A pdb=" N PHE F 231 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG F 233 " --> pdb=" O ASP F 229 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA F 234 " --> pdb=" O ILE F 230 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 277 Processing helix chain 'F' and resid 299 through 315 removed outlier: 4.088A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 312 " --> pdb=" O ASP F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 358 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 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 512 through 529 removed outlier: 3.886A pdb=" N LEU F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 559 Processing helix chain 'F' and resid 578 through 594 removed outlier: 3.553A pdb=" N GLN F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 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: 3.925A 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: 3.888A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 694 " --> pdb=" O GLU F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 719 removed outlier: 4.074A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET F 716 " --> pdb=" O MET F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 735 Processing helix chain 'H' and resid 20 through 34 removed outlier: 3.540A pdb=" N ARG H 30 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET H 32 " --> pdb=" O THR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 71 removed outlier: 3.818A pdb=" N ARG H 45 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 143 through 201 removed outlier: 3.561A pdb=" N GLY H 158 " --> pdb=" O SER H 154 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 183 " --> pdb=" O ASP H 179 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 236 removed outlier: 4.270A pdb=" N ILE I 202 " --> pdb=" O ARG I 198 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET I 229 " --> pdb=" O SER I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 251 removed outlier: 4.214A pdb=" N ARG I 246 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 75 removed outlier: 3.640A pdb=" N GLN J 34 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU J 54 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA J 72 " --> pdb=" O ASP J 68 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 Processing helix chain 'K' and resid 12 through 18 Processing helix chain 'K' and resid 35 through 54 Processing helix chain 'K' and resid 58 through 74 removed outlier: 4.459A pdb=" N LEU K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN K 74 " --> pdb=" O GLN K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 94 removed outlier: 3.818A pdb=" N ALA K 82 " --> pdb=" O LYS K 78 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR K 83 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 113 removed outlier: 3.794A pdb=" N GLU K 109 " --> pdb=" O MET K 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 133 removed outlier: 4.044A pdb=" N SER K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 155 removed outlier: 4.155A pdb=" N ALA K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 175 removed outlier: 3.878A pdb=" N LEU K 165 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN K 174 " --> pdb=" O GLY K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 194 removed outlier: 4.043A pdb=" N SER K 191 " --> pdb=" O GLN K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 211 Processing helix chain 'K' and resid 220 through 227 Processing helix chain 'K' and resid 235 through 237 No H-bonds generated for 'chain 'K' and resid 235 through 237' Processing helix chain 'K' and resid 242 through 252 removed outlier: 4.605A pdb=" N GLU K 249 " --> pdb=" O LYS K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 269 removed outlier: 3.878A pdb=" N VAL K 263 " --> pdb=" O TYR K 259 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE K 269 " --> pdb=" O GLU K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 290 Processing helix chain 'L' and resid 11 through 18 removed outlier: 3.581A pdb=" N ALA L 15 " --> pdb=" O MET L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 54 removed outlier: 3.699A pdb=" N LYS L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 72 removed outlier: 3.642A pdb=" N HIS L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 92 removed outlier: 3.527A pdb=" N PHE L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 114 removed outlier: 4.236A pdb=" N ASP L 113 " --> pdb=" O GLU L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 133 removed outlier: 3.547A pdb=" N ILE L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 154 Processing helix chain 'L' and resid 158 through 169 removed outlier: 3.768A pdb=" N LYS L 167 " --> pdb=" O LYS L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 181 No H-bonds generated for 'chain 'L' and resid 178 through 181' Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'L' and resid 199 through 208 removed outlier: 3.801A pdb=" N LYS L 203 " --> pdb=" O LYS L 199 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP L 204 " --> pdb=" O TYR L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 227 removed outlier: 3.977A pdb=" N VAL L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN L 226 " --> pdb=" O LYS L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 253 removed outlier: 3.558A pdb=" N ALA L 250 " --> pdb=" O LYS L 246 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS L 251 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU L 252 " --> pdb=" O LEU L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 267 removed outlier: 3.679A pdb=" N LYS L 264 " --> pdb=" O THR L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 291 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.589A pdb=" N VAL A 60 " --> pdb=" O ALA A 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 22 through 24 Processing sheet with id= D, first strand: chain 'A' and resid 182 through 185 removed outlier: 6.814A pdb=" N GLU A 153 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET A 95 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP A 151 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.613A pdb=" N GLN A 128 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 391 through 394 removed outlier: 4.278A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE A 256 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS A 323 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE A 370 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 283 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 326 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 539 through 543 removed outlier: 6.936A pdb=" N THR A 663 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU A 542 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 665 " --> pdb=" O GLU A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 565 through 568 removed outlier: 9.081A pdb=" N LYS A 566 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N CYS A 599 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N CYS A 568 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 601 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS A 639 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 600 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 641 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL A 602 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE A 643 " --> pdb=" O VAL A 602 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.535A pdb=" N ALA B 81 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS B 34 " --> pdb=" O TYR B 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.938A pdb=" N VAL B 60 " --> pdb=" O ALA B 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 182 through 187 removed outlier: 5.658A pdb=" N GLU B 98 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL B 149 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP B 100 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 147 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 128 through 131 Processing sheet with id= M, first strand: chain 'B' and resid 369 through 373 removed outlier: 3.549A pdb=" N THR B 373 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 283 through 285 Processing sheet with id= O, first strand: chain 'B' and resid 663 through 666 removed outlier: 3.595A pdb=" N LYS B 566 " --> pdb=" O CYS B 599 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 4 through 7 removed outlier: 12.525A pdb=" N GLU C 77 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER C 40 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.748A pdb=" N VAL C 60 " --> pdb=" O ALA C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 22 through 24 Processing sheet with id= S, first strand: chain 'C' and resid 182 through 187 removed outlier: 7.037A pdb=" N GLU C 153 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N MET C 95 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP C 151 " --> pdb=" O MET C 95 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= U, first strand: chain 'C' and resid 135 through 139 Processing sheet with id= V, first strand: chain 'C' and resid 371 through 373 removed outlier: 3.569A pdb=" N GLY C 260 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET C 393 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 259 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 323 through 326 removed outlier: 3.735A pdb=" N LEU C 368 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 663 through 666 removed outlier: 3.688A pdb=" N LEU C 540 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 541 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 644 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 4 through 7 Processing sheet with id= Z, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.621A pdb=" N VAL D 60 " --> pdb=" O ALA D 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 22 through 24 Processing sheet with id= AB, first strand: chain 'D' and resid 182 through 187 Processing sheet with id= AC, first strand: chain 'D' and resid 129 through 131 Processing sheet with id= AD, first strand: chain 'D' and resid 369 through 373 removed outlier: 3.687A pdb=" N THR D 373 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 260 " --> pdb=" O THR D 373 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 663 through 667 removed outlier: 6.773A pdb=" N LEU D 640 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL D 539 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLY D 543 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR D 646 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 598 " --> pdb=" O LYS D 639 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS D 566 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 601 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS D 568 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 92 through 96 removed outlier: 7.101A pdb=" N GLU D 153 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET D 95 " --> pdb=" O ASP D 151 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP D 151 " --> pdb=" O MET D 95 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 324 through 328 removed outlier: 6.767A pdb=" N LEU E 368 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE E 327 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE E 370 " --> pdb=" O PHE E 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'E' and resid 540 through 542 removed outlier: 8.390A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 324 through 328 removed outlier: 6.512A pdb=" N LEU F 368 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE F 327 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE F 370 " --> pdb=" O PHE F 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 536 through 542 removed outlier: 6.723A pdb=" N LEU F 640 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU F 541 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY F 644 " --> pdb=" O LEU F 541 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL F 600 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR F 645 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL F 602 " --> pdb=" O THR F 645 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS F 566 " --> pdb=" O VAL F 601 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ 1306 hydrogen bonds defined for protein. 3780 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: 27.26 Time building geometry restraints manager: 53.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 36542 1.02 - 1.22: 83 1.22 - 1.42: 14796 1.42 - 1.62: 21946 1.62 - 1.83: 358 Bond restraints: 73725 Sorted by residual: bond pdb=" C4 ATP B 802 " pdb=" N9 ATP B 802 " ideal model delta sigma weight residual 1.374 1.296 0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP D 802 " pdb=" N7 ATP D 802 " ideal model delta sigma weight residual 1.387 1.315 0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C4 ATP D 802 " pdb=" C5 ATP D 802 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 ... (remaining 73720 not shown) Histogram of bond angle deviations from ideal: 81.45 - 92.68: 11 92.68 - 103.90: 788 103.90 - 115.13: 94534 115.13 - 126.35: 37776 126.35 - 137.58: 601 Bond angle restraints: 133710 Sorted by residual: angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 107.48 29.35 1.00e+00 1.00e+00 8.61e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 111.56 28.31 1.00e+00 1.00e+00 8.02e+02 angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 112.29 27.58 1.00e+00 1.00e+00 7.61e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 113.97 25.90 1.00e+00 1.00e+00 6.71e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 114.03 25.84 1.00e+00 1.00e+00 6.68e+02 ... (remaining 133705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 28860 35.96 - 71.92: 165 71.92 - 107.89: 15 107.89 - 143.85: 4 143.85 - 179.81: 3 Dihedral angle restraints: 29047 sinusoidal: 14089 harmonic: 14958 Sorted by residual: dihedral pdb=" CD ARG A 388 " pdb=" NE ARG A 388 " pdb=" CZ ARG A 388 " pdb=" NH1 ARG A 388 " ideal model delta sinusoidal sigma weight residual 0.00 -179.81 179.81 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA LEU K 75 " pdb=" C LEU K 75 " pdb=" N GLN K 76 " pdb=" CA GLN K 76 " ideal model delta harmonic sigma weight residual 180.00 142.83 37.17 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA PHE L 206 " pdb=" C PHE L 206 " pdb=" N PHE L 207 " pdb=" CA PHE L 207 " ideal model delta harmonic sigma weight residual 180.00 143.18 36.82 0 5.00e+00 4.00e-02 5.42e+01 ... (remaining 29044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.560: 5668 0.560 - 1.121: 0 1.121 - 1.681: 2 1.681 - 2.241: 1 2.241 - 2.801: 1 Chirality restraints: 5672 Sorted by residual: chirality pdb=" CG LEU C 484 " pdb=" CB LEU C 484 " pdb=" CD1 LEU C 484 " pdb=" CD2 LEU C 484 " both_signs ideal model delta sigma weight residual False -2.59 0.21 -2.80 2.00e-01 2.50e+01 1.96e+02 chirality pdb=" CB VAL F 698 " pdb=" CA VAL F 698 " pdb=" CG1 VAL F 698 " pdb=" CG2 VAL F 698 " both_signs ideal model delta sigma weight residual False -2.63 -0.91 -1.72 2.00e-01 2.50e+01 7.42e+01 chirality pdb=" CB VAL B 346 " pdb=" CA VAL B 346 " pdb=" CG1 VAL B 346 " pdb=" CG2 VAL B 346 " both_signs ideal model delta sigma weight residual False -2.63 -1.03 -1.60 2.00e-01 2.50e+01 6.38e+01 ... (remaining 5669 not shown) Planarity restraints: 10896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 495 " 0.060 2.00e-02 2.50e+03 7.80e-02 9.14e+01 pdb=" CG ASN B 495 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 495 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 495 " -0.125 2.00e-02 2.50e+03 pdb="HD21 ASN B 495 " -0.012 2.00e-02 2.50e+03 pdb="HD22 ASN B 495 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 495 " -0.060 2.00e-02 2.50e+03 7.55e-02 8.55e+01 pdb=" CG ASN D 495 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN D 495 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 495 " 0.118 2.00e-02 2.50e+03 pdb="HD21 ASN D 495 " 0.008 2.00e-02 2.50e+03 pdb="HD22 ASN D 495 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 405 " -0.031 2.00e-02 2.50e+03 6.76e-02 6.85e+01 pdb=" CD GLN B 405 " 0.140 2.00e-02 2.50e+03 pdb=" OE1 GLN B 405 " -0.062 2.00e-02 2.50e+03 pdb=" NE2 GLN B 405 " -0.051 2.00e-02 2.50e+03 pdb="HE21 GLN B 405 " -0.011 2.00e-02 2.50e+03 pdb="HE22 GLN B 405 " 0.015 2.00e-02 2.50e+03 ... (remaining 10893 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 4157 2.18 - 2.79: 156120 2.79 - 3.39: 195660 3.39 - 4.00: 253869 4.00 - 4.60: 393326 Nonbonded interactions: 1003132 Sorted by model distance: nonbonded pdb="HH22 ARG E 607 " pdb=" O TYR E 611 " model vdw 1.579 1.850 nonbonded pdb=" O ASP L 267 " pdb="HH11 ARG L 271 " model vdw 1.579 1.850 nonbonded pdb=" O TYR A 499 " pdb=" H ILE A 503 " model vdw 1.586 1.850 nonbonded pdb=" OD1 ASP A 229 " pdb="HH21 ARG A 233 " model vdw 1.589 1.850 nonbonded pdb=" HZ2 LYS F 708 " pdb=" O3A ATP F 801 " model vdw 1.591 1.850 ... (remaining 1003127 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 1 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resid 7 \ 4 through 87 or (resid 88 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG \ 2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or nam \ e HZ3)) or resid 201 through 215 or (resid 216 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 217 through 457 or resi \ d 459 through 547 or (resid 548 and (name N or name CA or name C or name O or na \ me HA2 or name HA3)) or resid 549 through 738 or resid 801)) selection = (chain 'B' and (resid 1 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resid 7 \ 4 through 87 or (resid 88 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 201 or resi \ d 211 through 215 or (resid 216 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or na \ me HB3 or name HG2 or name HG3)) or resid 217 through 263 or (resid 264 and (nam \ e N or name CA or name C or name O or name CB or name SG or name HA or name HB2 \ or name HB3 or name HG )) or resid 265 through 387 or (resid 388 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name \ HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or \ name HH21)) or resid 389 through 457 or resid 459 or (resid 477 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE or name C \ Z or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 o \ r name HH22)) or resid 478 through 547 or (resid 548 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 549 through 738 or resid 801) \ ) selection = (chain 'C' and (resid 1 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 201 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA or nam \ e HB or name HG21 or name HG22 or name HG23)) or resid 211 through 263 or (resid \ 264 and (name N or name CA or name C or name O or name CB or name SG or name HA \ or name HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or \ name HH12 or name HH21)) or resid 389 through 457 or resid 470 or (resid 477 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 o \ r name HH21 or name HH22)) or resid 478 through 547 or (resid 548 and (name N or \ name CA or name C or name O or name HA2 or name HA3)) or resid 549 through 738 \ or resid 801)) selection = (chain 'D' and (resid 1 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resid 7 \ 4 through 87 or (resid 88 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG \ 2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or nam \ e HZ3)) or (resid 201 and (name N or name CA or name C or name O or name CB or n \ ame OG1 or name CG2 or name HA or name HB or name HG21 or name HG22 or name HG23 \ )) or resid 211 through 215 or (resid 216 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or name \ HB2 or name HB3 or name HG2 or name HG3)) or resid 217 through 263 or (resid 26 \ 4 and (name N or name CA or name C or name O or name CB or name SG or name HA or \ name HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH12 or name HH21)) or resid 389 through 457 or resid 470 or (resid 477 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or n \ ame HH21 or name HH22)) or resid 478 through 738 or resid 801)) } ncs_group { reference = (chain 'E' and (resid 219 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 224 through 237 or (r \ esid 238 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 239 or (resid 251 through 252 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 253 or (resid 254 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 25 \ 5 through 265 or (resid 266 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 267 through 268 or (resid 269 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 270 thro \ ugh 274 or (resid 275 through 278 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 279 or (resid 280 through 281 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 28 \ 2 or (resid 283 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 284 through 288 or (resid 289 through 295 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 296 or ( \ resid 297 through 298 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 299 through 301 or (resid 302 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 303 through 32 \ 4 or (resid 325 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 326 through 328 or (resid 329 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 330 or (resid 347 an \ d (name N or name CA or name C or name O or name CB or name HA )) or (resid 348 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 349 through 351 or (resid 352 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 353 through 358 or (resid 359 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 360 or (resid 361 through 364 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 365 or (resid 366 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 367 through 382 o \ r (resid 383 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 384 through 389 or (resid 390 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 398 through 414 or resi \ d 422 through 457 or (resid 471 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or na \ me HB3 or name HG2 or name HG3)) or resid 472 through 738 or resid 801)) selection = chain 'F' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 8 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD21)) or resid 51 through 221 or (resid 222 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 223 through 292 or (resid 293 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 S 210 5.16 5 C 22976 2.51 5 N 6342 2.21 5 O 7008 1.98 5 H 36604 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.810 Extract box with map and model: 7.910 Check model and map are aligned: 0.820 Convert atoms to be neutral: 0.500 Process input model: 187.940 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.130 37121 Z= 0.826 Angle : 1.546 29.349 50060 Z= 0.936 Chirality : 0.094 2.801 5672 Planarity : 0.009 0.128 6447 Dihedral : 11.448 179.810 14064 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.90 % Favored : 95.82 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.10), residues: 4589 helix: -2.56 (0.09), residues: 1967 sheet: -2.31 (0.17), residues: 593 loop : -2.08 (0.12), residues: 2029 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 4.742 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 outliers start: 4 outliers final: 3 residues processed: 280 average time/residue: 1.0706 time to fit residues: 476.1205 Evaluate side-chains 221 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 4.691 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.8870 time to fit residues: 10.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 387 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 359 optimal weight: 2.9990 chunk 139 optimal weight: 40.0000 chunk 218 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 416 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 435 ASN B 505 ASN B 659 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 190 ASN C 374 ASN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN D 301 ASN D 435 ASN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 ASN D 659 ASN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN E 719 GLN F 286 ASN F 313 GLN F 675 GLN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN L 63 ASN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 254 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 37121 Z= 0.207 Angle : 0.679 11.812 50060 Z= 0.363 Chirality : 0.060 1.891 5672 Planarity : 0.004 0.051 6447 Dihedral : 8.894 179.336 4985 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: -2.74 (0.11), residues: 4589 helix: -1.73 (0.10), residues: 1995 sheet: -1.89 (0.18), residues: 588 loop : -1.71 (0.13), residues: 2006 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 4.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1 residues processed: 260 average time/residue: 1.0556 time to fit residues: 425.9935 Evaluate side-chains 233 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 4.757 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6077 time to fit residues: 7.1351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 231 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 346 optimal weight: 6.9990 chunk 283 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 417 optimal weight: 9.9990 chunk 451 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 414 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 505 ASN B 659 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN E 301 ASN ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 ASN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 37121 Z= 0.326 Angle : 0.703 10.971 50060 Z= 0.390 Chirality : 0.058 1.769 5672 Planarity : 0.005 0.053 6447 Dihedral : 8.481 176.142 4985 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.73 % Favored : 94.23 % 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: -2.36 (0.11), residues: 4589 helix: -1.29 (0.10), residues: 2011 sheet: -1.59 (0.18), residues: 624 loop : -1.70 (0.13), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 4.918 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: 1 outliers final: 1 residues processed: 240 average time/residue: 1.0818 time to fit residues: 410.5888 Evaluate side-chains 218 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 4.831 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7862 time to fit residues: 7.2623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 412 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 280 optimal weight: 30.0000 chunk 419 optimal weight: 4.9990 chunk 443 optimal weight: 20.0000 chunk 218 optimal weight: 50.0000 chunk 397 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 37121 Z= 0.242 Angle : 0.611 10.956 50060 Z= 0.332 Chirality : 0.057 1.770 5672 Planarity : 0.004 0.046 6447 Dihedral : 8.224 177.212 4985 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.11), residues: 4589 helix: -0.99 (0.11), residues: 2028 sheet: -1.47 (0.19), residues: 618 loop : -1.59 (0.13), residues: 1943 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 4.960 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: 0 outliers final: 0 residues processed: 231 average time/residue: 1.0086 time to fit residues: 365.7736 Evaluate side-chains 212 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 4.754 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 369 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 226 optimal weight: 30.0000 chunk 398 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 374 ASN B 659 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 37121 Z= 0.338 Angle : 0.700 10.666 50060 Z= 0.386 Chirality : 0.057 1.739 5672 Planarity : 0.005 0.050 6447 Dihedral : 8.281 179.944 4985 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 26.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.11), residues: 4589 helix: -1.27 (0.10), residues: 2057 sheet: -1.50 (0.20), residues: 608 loop : -1.62 (0.14), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 4.817 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: 0 outliers final: 0 residues processed: 223 average time/residue: 1.0460 time to fit residues: 370.6113 Evaluate side-chains 207 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 4.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 149 optimal weight: 8.9990 chunk 399 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 260 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 444 optimal weight: 20.0000 chunk 368 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 505 ASN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 37121 Z= 0.244 Angle : 0.603 10.847 50060 Z= 0.328 Chirality : 0.056 1.765 5672 Planarity : 0.004 0.050 6447 Dihedral : 8.085 178.757 4985 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.12), residues: 4589 helix: -1.01 (0.11), residues: 2066 sheet: -1.48 (0.20), residues: 605 loop : -1.55 (0.14), residues: 1918 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 4.825 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: 0 outliers final: 0 residues processed: 223 average time/residue: 1.0028 time to fit residues: 355.2050 Evaluate side-chains 212 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 4.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 428 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 442 optimal weight: 9.9990 chunk 276 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 37121 Z= 0.222 Angle : 0.588 10.787 50060 Z= 0.317 Chirality : 0.056 1.749 5672 Planarity : 0.004 0.054 6447 Dihedral : 7.952 177.564 4985 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.00 % 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: -1.85 (0.12), residues: 4589 helix: -0.80 (0.11), residues: 2065 sheet: -1.44 (0.20), residues: 605 loop : -1.47 (0.14), residues: 1919 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 4.877 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: 0 outliers final: 0 residues processed: 224 average time/residue: 1.0413 time to fit residues: 373.0008 Evaluate side-chains 213 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 4.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 273 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 301 optimal weight: 5.9990 chunk 218 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 347 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 301 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 37121 Z= 0.174 Angle : 0.556 10.880 50060 Z= 0.294 Chirality : 0.056 1.739 5672 Planarity : 0.003 0.042 6447 Dihedral : 7.782 177.706 4985 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % 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: 4589 helix: -0.45 (0.11), residues: 2048 sheet: -1.29 (0.20), residues: 612 loop : -1.39 (0.14), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 4.785 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: 1 outliers final: 0 residues processed: 223 average time/residue: 0.9902 time to fit residues: 351.6104 Evaluate side-chains 216 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 4.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 402 optimal weight: 30.0000 chunk 423 optimal weight: 10.0000 chunk 386 optimal weight: 4.9990 chunk 412 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 372 optimal weight: 8.9990 chunk 389 optimal weight: 8.9990 chunk 410 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 301 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 37121 Z= 0.217 Angle : 0.573 10.749 50060 Z= 0.309 Chirality : 0.056 1.724 5672 Planarity : 0.004 0.056 6447 Dihedral : 7.758 177.694 4985 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.12), residues: 4589 helix: -0.49 (0.11), residues: 2049 sheet: -1.33 (0.20), residues: 623 loop : -1.41 (0.14), residues: 1917 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 6.204 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 outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.9917 time to fit residues: 353.2746 Evaluate side-chains 208 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 270 optimal weight: 2.9990 chunk 435 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 457 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 281 optimal weight: 20.0000 chunk 223 optimal weight: 50.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 37121 Z= 0.300 Angle : 0.644 10.620 50060 Z= 0.355 Chirality : 0.056 1.748 5672 Planarity : 0.005 0.084 6447 Dihedral : 7.888 177.894 4985 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.12), residues: 4589 helix: -0.85 (0.11), residues: 2060 sheet: -1.47 (0.20), residues: 629 loop : -1.54 (0.14), residues: 1900 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 4.757 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: 220 average time/residue: 0.9840 time to fit residues: 347.2579 Evaluate side-chains 208 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 289 optimal weight: 5.9990 chunk 387 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 335 optimal weight: 50.0000 chunk 53 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 364 optimal weight: 9.9990 chunk 152 optimal weight: 40.0000 chunk 374 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.039510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.028382 restraints weight = 1820150.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.029293 restraints weight = 711624.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.029891 restraints weight = 364877.980| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 37121 Z= 0.202 Angle : 0.574 10.865 50060 Z= 0.307 Chirality : 0.056 1.731 5672 Planarity : 0.004 0.042 6447 Dihedral : 7.721 176.625 4985 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.12), residues: 4589 helix: -0.55 (0.11), residues: 2066 sheet: -1.42 (0.20), residues: 623 loop : -1.41 (0.14), residues: 1900 =============================================================================== Job complete usr+sys time: 9283.30 seconds wall clock time: 164 minutes 33.74 seconds (9873.74 seconds total)