Starting phenix.real_space_refine on Sun Feb 18 10:39:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/02_2024/6mdn_9101_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/02_2024/6mdn_9101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/02_2024/6mdn_9101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/02_2024/6mdn_9101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/02_2024/6mdn_9101_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/02_2024/6mdn_9101_trim_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 S 210 5.16 5 C 22882 2.51 5 N 6311 2.21 5 O 6980 1.98 5 H 36496 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 388": not complete - not flipped Residue "A ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 617": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 413": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B LEU 420": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "B ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 691": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C LEU 484": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "C ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 446": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 725": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 727": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72910 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 8082 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 11129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 11129 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 29, 'TRANS': 677} Chain breaks: 3 Chain: "C" Number of atoms: 11167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 11167 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 29, 'TRANS': 679} Chain breaks: 3 Chain: "D" Number of atoms: 11232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 11232 Classifications: {'peptide': 713} Link IDs: {'PTRANS': 29, 'TRANS': 683} Chain breaks: 3 Chain: "E" Number of atoms: 10987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 10987 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 26, 'TRANS': 670} Chain breaks: 4 Chain: "F" Number of atoms: 6748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6748 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 18, 'TRANS': 430} Chain breaks: 5 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2295 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1063 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "J" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 984 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4436 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 3, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4454 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 3, 'TRANS': 282} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.52, per 1000 atoms: 0.31 Number of scatterers: 72910 At special positions: 0 Unit cell: (154.58, 146.72, 227.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 210 16.00 P 31 15.00 O 6980 8.00 N 6311 7.00 C 22882 6.00 H 36496 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM72691 O3B ATP B 802 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 45.67 Conformation dependent library (CDL) restraints added in 5.5 seconds 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8652 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 35 sheets defined 44.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.07 Creating SS restraints... Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.282A pdb=" N GLN A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.739A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 295 through 316 removed outlier: 4.608A pdb=" N GLU A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 400 through 417 removed outlier: 4.395A pdb=" N ARG A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.805A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 455 removed outlier: 3.512A pdb=" N GLU A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 5.001A pdb=" N ASP A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 512 through 529 removed outlier: 3.973A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 558 Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.634A pdb=" N LYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.862A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.949A pdb=" N GLU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.788A pdb=" N ILE A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.886A pdb=" N GLU A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 114 through 124 Processing helix chain 'B' and resid 224 through 239 removed outlier: 3.505A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 297 through 315 removed outlier: 4.216A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 381 through 384 No H-bonds generated for 'chain 'B' and resid 381 through 384' Processing helix chain 'B' and resid 400 through 416 removed outlier: 3.859A pdb=" N LEU B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N MET B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 438 through 456 removed outlier: 3.972A pdb=" N GLU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 512 through 529 Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 578 through 594 removed outlier: 3.552A pdb=" N ALA B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.953A pdb=" N LYS B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 707 through 718 removed outlier: 3.932A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.204A pdb=" N VAL B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 87 through 90 No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.549A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.852A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 348 through 358 removed outlier: 3.554A pdb=" N SER C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 381 through 384 No H-bonds generated for 'chain 'C' and resid 381 through 384' Processing helix chain 'C' and resid 400 through 410 removed outlier: 3.545A pdb=" N LEU C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 439 through 456 Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 498 through 502 removed outlier: 3.736A pdb=" N TYR C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 502' Processing helix chain 'C' and resid 512 through 530 Processing helix chain 'C' and resid 550 through 560 removed outlier: 3.635A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 594 removed outlier: 3.622A pdb=" N LYS C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 620 through 630 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 688 through 698 removed outlier: 4.061A pdb=" N THR C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 removed outlier: 4.084A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 737 removed outlier: 4.403A pdb=" N GLU C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 236 through 239 No H-bonds generated for 'chain 'D' and resid 236 through 239' Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 266 through 275 removed outlier: 4.865A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 315 removed outlier: 4.093A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 358 removed outlier: 3.937A pdb=" N VAL D 351 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 355 " --> pdb=" O ASN D 352 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.950A pdb=" N HIS D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 removed outlier: 3.597A pdb=" N GLU D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.190A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 488 Processing helix chain 'D' and resid 512 through 530 removed outlier: 4.072A pdb=" N GLN D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.705A pdb=" N ALA D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 594 removed outlier: 4.023A pdb=" N MET D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 621 through 631 removed outlier: 3.901A pdb=" N LYS D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 652 through 655 No H-bonds generated for 'chain 'D' and resid 652 through 655' Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 688 through 695 Processing helix chain 'D' and resid 707 through 719 removed outlier: 4.263A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 736 removed outlier: 3.982A pdb=" N VAL D 726 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 736 " --> pdb=" O LEU D 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 114 through 122 removed outlier: 3.926A pdb=" N ILE E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 266 through 277 Processing helix chain 'E' and resid 297 through 316 removed outlier: 4.364A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 333 No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 380 through 383 No H-bonds generated for 'chain 'E' and resid 380 through 383' Processing helix chain 'E' and resid 400 through 410 Processing helix chain 'E' and resid 412 through 415 No H-bonds generated for 'chain 'E' and resid 412 through 415' Processing helix chain 'E' and resid 426 through 432 removed outlier: 4.521A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 454 removed outlier: 3.889A pdb=" N ALA E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 512 through 530 Processing helix chain 'E' and resid 549 through 560 Processing helix chain 'E' and resid 570 through 573 Processing helix chain 'E' and resid 578 through 583 Processing helix chain 'E' and resid 585 through 593 Processing helix chain 'E' and resid 605 through 609 Processing helix chain 'E' and resid 620 through 631 removed outlier: 4.834A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 655 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 688 through 697 removed outlier: 3.780A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 719 removed outlier: 3.578A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 735 removed outlier: 4.179A pdb=" N ALA E 731 " --> pdb=" O ARG E 727 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 735 " --> pdb=" O ALA E 731 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 238 removed outlier: 3.570A pdb=" N PHE F 231 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 233 " --> pdb=" O ASP F 229 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA F 234 " --> pdb=" O ILE F 230 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 277 removed outlier: 3.588A pdb=" N GLY F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 315 removed outlier: 4.071A pdb=" N ARG F 303 " --> pdb=" O GLU F 299 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 359 removed outlier: 4.483A pdb=" N ASN F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F 358 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 410 Processing helix chain 'F' and resid 428 through 431 No H-bonds generated for 'chain 'F' and resid 428 through 431' Processing helix chain 'F' and resid 433 through 435 No H-bonds generated for 'chain 'F' and resid 433 through 435' Processing helix chain 'F' and resid 444 through 447 No H-bonds generated for 'chain 'F' and resid 444 through 447' Processing helix chain 'F' and resid 450 through 453 No H-bonds generated for 'chain 'F' and resid 450 through 453' Processing helix chain 'F' and resid 499 through 502 No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 512 through 529 removed outlier: 4.008A pdb=" N LEU F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 559 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 578 through 594 removed outlier: 3.555A pdb=" N GLN F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 620 through 631 removed outlier: 3.627A pdb=" N LYS F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 655 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 688 through 696 removed outlier: 3.826A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 694 " --> pdb=" O GLU F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 719 removed outlier: 4.095A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET F 716 " --> pdb=" O MET F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 735 Processing helix chain 'H' and resid 20 through 34 removed outlier: 3.575A pdb=" N SER H 25 " --> pdb=" O ALA H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 82 removed outlier: 3.779A pdb=" N LEU H 57 " --> pdb=" O GLN H 53 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP H 58 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU H 75 " --> pdb=" O MET H 71 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 201 removed outlier: 3.847A pdb=" N GLU H 148 " --> pdb=" O ASN H 144 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU H 151 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY H 158 " --> pdb=" O SER H 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN H 159 " --> pdb=" O GLY H 155 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU H 170 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE H 171 " --> pdb=" O MET H 167 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU H 183 " --> pdb=" O ASP H 179 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS H 184 " --> pdb=" O ARG H 180 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 236 removed outlier: 4.297A pdb=" N ILE I 202 " --> pdb=" O ARG I 198 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET I 229 " --> pdb=" O SER I 225 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE I 230 " --> pdb=" O GLN I 226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP I 231 " --> pdb=" O GLY I 227 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR I 235 " --> pdb=" O ASP I 231 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN I 236 " --> pdb=" O ARG I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 254 removed outlier: 3.904A pdb=" N ARG I 246 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS I 253 " --> pdb=" O SER I 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 67 removed outlier: 3.646A pdb=" N VAL J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG J 66 " --> pdb=" O GLU J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 85 removed outlier: 3.754A pdb=" N GLY J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 16 Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.678A pdb=" N GLU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA K 55 " --> pdb=" O MET K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 74 removed outlier: 3.841A pdb=" N ASN K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN K 74 " --> pdb=" O GLN K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 94 removed outlier: 4.085A pdb=" N PHE K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 114 removed outlier: 3.657A pdb=" N ILE K 108 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU K 109 " --> pdb=" O MET K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 133 removed outlier: 3.800A pdb=" N SER K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 155 removed outlier: 4.425A pdb=" N ALA K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 175 removed outlier: 3.972A pdb=" N TYR K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN K 174 " --> pdb=" O GLY K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 194 removed outlier: 3.931A pdb=" N ASP K 194 " --> pdb=" O THR K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 211 Processing helix chain 'K' and resid 220 through 227 Processing helix chain 'K' and resid 235 through 238 Processing helix chain 'K' and resid 242 through 252 removed outlier: 4.343A pdb=" N GLU K 249 " --> pdb=" O LYS K 245 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA K 250 " --> pdb=" O LYS K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.808A pdb=" N THR K 260 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU K 261 " --> pdb=" O ASP K 257 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER K 262 " --> pdb=" O SER K 258 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL K 263 " --> pdb=" O TYR K 259 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU K 265 " --> pdb=" O GLU K 261 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 291 Processing helix chain 'L' and resid 10 through 20 removed outlier: 3.693A pdb=" N LEU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA L 15 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 54 removed outlier: 3.612A pdb=" N ASN L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.725A pdb=" N ALA L 69 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 94 removed outlier: 3.694A pdb=" N LYS L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 111 removed outlier: 3.899A pdb=" N ILE L 110 " --> pdb=" O ARG L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 133 removed outlier: 4.199A pdb=" N HIS L 123 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 154 removed outlier: 3.565A pdb=" N GLN L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 170 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 185 through 193 removed outlier: 3.721A pdb=" N GLY L 189 " --> pdb=" O TYR L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 211 removed outlier: 4.687A pdb=" N LYS L 203 " --> pdb=" O TYR L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 227 removed outlier: 4.469A pdb=" N VAL L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN L 226 " --> pdb=" O LYS L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 251 Processing helix chain 'L' and resid 257 through 267 removed outlier: 3.764A pdb=" N VAL L 263 " --> pdb=" O TYR L 259 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS L 264 " --> pdb=" O THR L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 291 removed outlier: 3.758A pdb=" N THR L 286 " --> pdb=" O ARG L 282 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE L 287 " --> pdb=" O ILE L 283 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN L 288 " --> pdb=" O LYS L 284 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP L 290 " --> pdb=" O THR L 286 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 392 through 395 removed outlier: 9.320A pdb=" N MET A 393 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 257 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 395 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR A 259 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 256 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY A 260 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR A 373 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS A 323 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 370 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 283 " --> pdb=" O ILE A 326 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 663 through 666 removed outlier: 3.521A pdb=" N THR A 663 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 540 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 640 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL A 539 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE A 642 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU A 541 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 644 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 566 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= D, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.069A pdb=" N VAL B 60 " --> pdb=" O ALA B 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 22 through 24 Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.667A pdb=" N GLU B 153 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B 95 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 151 " --> pdb=" O MET B 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= I, first strand: chain 'B' and resid 135 through 140 Processing sheet with id= J, first strand: chain 'B' and resid 369 through 373 removed outlier: 3.562A pdb=" N THR B 373 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 260 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 283 through 285 Processing sheet with id= L, first strand: chain 'B' and resid 663 through 666 removed outlier: 8.705A pdb=" N VAL B 539 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 642 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 541 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY B 644 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 566 " --> pdb=" O CYS B 599 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.554A pdb=" N ALA C 81 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.467A pdb=" N VAL C 60 " --> pdb=" O ALA C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 182 through 187 removed outlier: 5.612A pdb=" N GLU C 98 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL C 149 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP C 100 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU C 147 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 131 Processing sheet with id= Q, first strand: chain 'C' and resid 391 through 395 removed outlier: 6.803A pdb=" N GLY C 371 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY C 260 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR C 373 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 323 through 326 removed outlier: 3.654A pdb=" N LEU C 368 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 663 through 667 removed outlier: 6.630A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU C 541 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY C 644 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY C 543 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR C 646 " --> pdb=" O GLY C 543 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 4 through 7 removed outlier: 12.652A pdb=" N GLU D 77 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N SER D 40 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 24 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.242A pdb=" N VAL D 60 " --> pdb=" O ALA D 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 182 through 187 Processing sheet with id= W, first strand: chain 'D' and resid 129 through 131 Processing sheet with id= X, first strand: chain 'D' and resid 170 through 172 removed outlier: 4.346A pdb=" N GLN D 170 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE D 152 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP D 151 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 392 through 394 removed outlier: 9.045A pdb=" N MET D 393 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 257 " --> pdb=" O MET D 393 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL D 369 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU D 258 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY D 371 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 663 through 667 removed outlier: 6.562A pdb=" N LEU D 640 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL D 539 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY D 543 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR D 646 " --> pdb=" O GLY D 543 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= AB, first strand: chain 'E' and resid 8 through 10 removed outlier: 6.530A pdb=" N VAL E 60 " --> pdb=" O ALA E 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 182 through 187 Processing sheet with id= AD, first strand: chain 'E' and resid 128 through 131 Processing sheet with id= AE, first strand: chain 'E' and resid 283 through 285 removed outlier: 3.681A pdb=" N LYS E 283 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU E 368 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE E 327 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE E 370 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 540 through 542 removed outlier: 7.981A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 603 " --> pdb=" O CYS E 568 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 92 through 96 removed outlier: 7.099A pdb=" N GLU E 153 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET E 95 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP E 151 " --> pdb=" O MET E 95 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 283 through 286 removed outlier: 6.761A pdb=" N ILE F 324 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASN F 286 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 326 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 368 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 325 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 370 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 536 through 542 removed outlier: 6.846A pdb=" N LEU F 640 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU F 541 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY F 644 " --> pdb=" O LEU F 541 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 600 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR F 645 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL F 602 " --> pdb=" O THR F 645 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI 1307 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.12 Time building geometry restraints manager: 48.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 36434 1.01 - 1.22: 82 1.22 - 1.42: 14797 1.42 - 1.62: 21788 1.62 - 1.83: 358 Bond restraints: 73459 Sorted by residual: bond pdb=" C4 ATP B 802 " pdb=" N9 ATP B 802 " ideal model delta sigma weight residual 1.374 1.288 0.086 1.00e-02 1.00e+04 7.41e+01 bond pdb=" C5 ATP D 802 " pdb=" N7 ATP D 802 " ideal model delta sigma weight residual 1.387 1.313 0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C4 ATP B 801 " pdb=" N9 ATP B 801 " ideal model delta sigma weight residual 1.374 1.303 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C4 ATP D 801 " pdb=" N9 ATP D 801 " ideal model delta sigma weight residual 1.374 1.304 0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C4 ATP C 801 " pdb=" N9 ATP C 801 " ideal model delta sigma weight residual 1.374 1.305 0.069 1.00e-02 1.00e+04 4.74e+01 ... (remaining 73454 not shown) Histogram of bond angle deviations from ideal: 78.06 - 89.92: 28 89.92 - 101.79: 189 101.79 - 113.65: 90116 113.65 - 125.52: 41457 125.52 - 137.39: 1445 Bond angle restraints: 133235 Sorted by residual: angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 107.81 29.02 1.00e+00 1.00e+00 8.42e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 112.32 27.55 1.00e+00 1.00e+00 7.59e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 112.50 27.37 1.00e+00 1.00e+00 7.49e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 113.20 26.67 1.00e+00 1.00e+00 7.12e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 115.05 24.82 1.00e+00 1.00e+00 6.16e+02 ... (remaining 133230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 33582 35.92 - 71.84: 634 71.84 - 107.76: 29 107.76 - 143.68: 5 143.68 - 179.60: 2 Dihedral angle restraints: 34252 sinusoidal: 19323 harmonic: 14929 Sorted by residual: dihedral pdb=" CA PRO D 613 " pdb=" C PRO D 613 " pdb=" N ILE D 614 " pdb=" CA ILE D 614 " ideal model delta harmonic sigma weight residual 180.00 101.31 78.69 0 5.00e+00 4.00e-02 2.48e+02 dihedral pdb=" CD ARG A 388 " pdb=" NE ARG A 388 " pdb=" CZ ARG A 388 " pdb=" NH1 ARG A 388 " ideal model delta sinusoidal sigma weight residual 0.00 -179.60 179.60 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA GLN B 496 " pdb=" C GLN B 496 " pdb=" N GLU B 497 " pdb=" CA GLU B 497 " ideal model delta harmonic sigma weight residual 180.00 122.10 57.90 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 34249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.596: 5643 0.596 - 1.191: 2 1.191 - 1.787: 3 1.787 - 2.382: 1 2.382 - 2.978: 2 Chirality restraints: 5651 Sorted by residual: chirality pdb=" CG LEU C 484 " pdb=" CB LEU C 484 " pdb=" CD1 LEU C 484 " pdb=" CD2 LEU C 484 " both_signs ideal model delta sigma weight residual False -2.59 0.39 -2.98 2.00e-01 2.50e+01 2.22e+02 chirality pdb=" CG LEU B 420 " pdb=" CB LEU B 420 " pdb=" CD1 LEU B 420 " pdb=" CD2 LEU B 420 " both_signs ideal model delta sigma weight residual False -2.59 0.21 -2.80 2.00e-01 2.50e+01 1.96e+02 chirality pdb=" CG LEU B 682 " pdb=" CB LEU B 682 " pdb=" CD1 LEU B 682 " pdb=" CD2 LEU B 682 " both_signs ideal model delta sigma weight residual False -2.59 -0.65 -1.93 2.00e-01 2.50e+01 9.36e+01 ... (remaining 5648 not shown) Planarity restraints: 10852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 279 " -0.031 2.00e-02 2.50e+03 6.59e-02 4.34e+01 pdb=" C ALA F 279 " 0.114 2.00e-02 2.50e+03 pdb=" O ALA F 279 " -0.045 2.00e-02 2.50e+03 pdb=" N ARG F 280 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 199 " -0.029 2.00e-02 2.50e+03 6.38e-02 4.07e+01 pdb=" C ALA C 199 " 0.110 2.00e-02 2.50e+03 pdb=" O ALA C 199 " -0.044 2.00e-02 2.50e+03 pdb=" N LYS C 200 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 480 " -0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C PHE B 480 " 0.094 2.00e-02 2.50e+03 pdb=" O PHE B 480 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU B 481 " -0.032 2.00e-02 2.50e+03 ... (remaining 10849 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.90: 385 1.90 - 2.58: 84197 2.58 - 3.25: 221795 3.25 - 3.93: 272749 3.93 - 4.60: 431056 Nonbonded interactions: 1010182 Sorted by model distance: nonbonded pdb=" ND2 ASN E 435 " pdb="HD21 ASN E 495 " model vdw 1.231 2.600 nonbonded pdb=" HG2 ARG F 315 " pdb="HD11 LEU F 316 " model vdw 1.447 2.440 nonbonded pdb=" HG2 ARG F 315 " pdb="HD12 LEU F 316 " model vdw 1.466 2.440 nonbonded pdb=" O GLU F 297 " pdb=" H ASN F 301 " model vdw 1.519 1.850 nonbonded pdb=" O LEU K 219 " pdb=" H LEU K 223 " model vdw 1.543 1.850 ... (remaining 1010177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 219 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 224 through 237 or (r \ esid 238 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 239 or (resid 251 through 252 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 253 or (resid 254 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 25 \ 5 through 265 or (resid 266 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 267 through 268 or (resid 269 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 270 thro \ ugh 274 or (resid 275 through 278 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 279 or (resid 280 through 281 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 28 \ 2 or (resid 283 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 284 through 288 or (resid 289 through 295 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 296 or ( \ resid 297 through 298 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 299 through 301 or (resid 302 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 303 through 32 \ 4 or (resid 325 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 326 through 328 or (resid 329 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 330 or (resid 347 an \ d (name N or name CA or name C or name O or name CB or name HA )) or (resid 348 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 349 through 351 or (resid 352 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 353 through 358 or (resid 359 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 360 or (resid 361 through 364 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 365 or (resid 366 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 367 through 373 o \ r resid 398 through 414 or resid 422 through 457 or resid 477 through 738 or res \ id 801)) selection = (chain 'F' and (resid 219 through 263 or (resid 264 and (name N or name CA or na \ me C or name O or name CB or name SG or name HA or name HB2 or name HB3 or name \ HG )) or resid 265 through 322 or (resid 323 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 32 \ 4 through 457 or resid 477 through 738 or resid 801)) } ncs_group { reference = (chain 'B' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 11 through \ 72 or (resid 73 and (name N or name CA or name C or name O or name CB or name O \ G or name H or name HA or name HB2 or name HB3)) or resid 74 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB or name HA or name HB \ 1 or name HB2 or name HB3)) or resid 89 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or resid 201 \ or resid 215 through 240 or resid 250 through 457 or resid 459 through 547 or (r \ esid 548 and (name N or name CA or name C or name O or name HA2 or name HA3)) or \ resid 549 through 738 or resid 801)) selection = (chain 'C' and (resid 1 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 74 through 87 or (resid 88 and (name N or name CA or name C or name O o \ r name CB or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 2 \ 01 or resid 215 through 240 or resid 250 through 457 or resid 470 or resid 472 o \ r (resid 475 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23)) or resid 476 through 547 or (resid 548 and (nam \ e N or name CA or name C or name O or name HA2 or name HA3)) or resid 549 throug \ h 738 or resid 801)) selection = (chain 'D' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 11 through \ 199 or (resid 200 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or nam \ e HZ1 or name HZ3)) or resid 201 or resid 215 through 240 or resid 250 through 4 \ 57 or resid 470 or resid 472 or (resid 475 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or n \ ame HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 476 thro \ ugh 738 or resid 801)) selection = (chain 'E' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 11 through \ 72 or (resid 73 and (name N or name CA or name C or name O or name CB or name O \ G or name H or name HA or name HB2 or name HB3)) or resid 74 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB or name HA or name HB \ 1 or name HB2 or name HB3)) or resid 89 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 201 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2 o \ r name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 215 throu \ gh 457 or resid 470 or resid 472 or (resid 475 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 476 \ through 547 or (resid 548 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 549 through 738 or resid 801)) } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 8 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 117 thr \ ough 158 or (resid 159 and (name N or name CA or name C or name O or name CB or \ name OG or name H or name HA or name HB2 or name HB3)) or resid 160 through 221 \ or (resid 222 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 223 through 293)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.840 Extract box with map and model: 5.470 Check model and map are aligned: 0.800 Set scattering table: 0.490 Process input model: 175.020 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.152 36963 Z= 1.050 Angle : 1.673 29.023 49842 Z= 1.011 Chirality : 0.116 2.978 5651 Planarity : 0.009 0.076 6415 Dihedral : 12.419 179.603 14281 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.82 % Favored : 96.94 % Rotamer: Outliers : 0.38 % Allowed : 4.89 % Favored : 94.72 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.10), residues: 4570 helix: -2.68 (0.09), residues: 2040 sheet: -2.06 (0.16), residues: 622 loop : -2.06 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP B 510 HIS 0.027 0.005 HIS K 213 PHE 0.066 0.007 PHE A 589 TYR 0.060 0.006 TYR F 593 ARG 0.026 0.003 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 277 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 724 TYR cc_start: 0.7384 (m-80) cc_final: 0.7170 (m-80) REVERT: C 155 MET cc_start: 0.7702 (mtm) cc_final: 0.7311 (mpp) REVERT: D 273 ILE cc_start: 0.9369 (mt) cc_final: 0.9149 (tp) REVERT: D 573 MET cc_start: 0.6589 (ptp) cc_final: 0.6349 (ptt) REVERT: F 354 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6324 (mt) REVERT: I 219 MET cc_start: 0.9354 (tmt) cc_final: 0.9055 (tpp) outliers start: 15 outliers final: 7 residues processed: 291 average time/residue: 1.0136 time to fit residues: 460.2044 Evaluate side-chains 225 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 7.9990 chunk 346 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 217 optimal weight: 0.5980 chunk 266 optimal weight: 50.0000 chunk 415 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 272 GLN C 374 ASN C 435 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 GLN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN D 697 GLN D 719 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN E 495 ASN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 ASN F 675 GLN H 159 ASN H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 HIS K 123 HIS ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36963 Z= 0.197 Angle : 0.687 11.349 49842 Z= 0.367 Chirality : 0.062 1.643 5651 Planarity : 0.005 0.064 6415 Dihedral : 11.096 179.466 5242 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 0.10 % Allowed : 1.46 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 4570 helix: -1.79 (0.10), residues: 2041 sheet: -1.58 (0.18), residues: 624 loop : -1.82 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 510 HIS 0.007 0.001 HIS L 144 PHE 0.022 0.002 PHE D 661 TYR 0.029 0.002 TYR F 593 ARG 0.017 0.001 ARG I 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 4.425 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: A 340 MET cc_start: 0.8148 (pmm) cc_final: 0.7892 (pmm) REVERT: D 495 ASN cc_start: 0.6540 (t0) cc_final: 0.5732 (m-40) REVERT: D 589 PHE cc_start: 0.7003 (m-10) cc_final: 0.6320 (m-10) REVERT: L 23 ASN cc_start: 0.8927 (m-40) cc_final: 0.8692 (m-40) outliers start: 4 outliers final: 2 residues processed: 265 average time/residue: 1.0306 time to fit residues: 429.3258 Evaluate side-chains 228 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 4.9990 chunk 128 optimal weight: 40.0000 chunk 345 optimal weight: 10.0000 chunk 282 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 415 optimal weight: 20.0000 chunk 449 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 412 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 333 optimal weight: 40.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 ASN L 254 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 36963 Z= 0.311 Angle : 0.669 10.932 49842 Z= 0.370 Chirality : 0.061 1.715 5651 Planarity : 0.004 0.056 6415 Dihedral : 10.674 179.012 5242 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 0.05 % Allowed : 1.56 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.11), residues: 4570 helix: -1.30 (0.10), residues: 2037 sheet: -1.45 (0.18), residues: 615 loop : -1.68 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 213 HIS 0.008 0.001 HIS B 666 PHE 0.023 0.002 PHE I 216 TYR 0.017 0.002 TYR B 611 ARG 0.006 0.001 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 4.353 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: D 589 PHE cc_start: 0.6712 (m-10) cc_final: 0.6135 (m-10) REVERT: E 1 MET cc_start: 0.8866 (ttt) cc_final: 0.8637 (tpp) REVERT: H 167 MET cc_start: 0.9171 (tmm) cc_final: 0.8966 (tmm) outliers start: 2 outliers final: 0 residues processed: 245 average time/residue: 0.9614 time to fit residues: 376.5944 Evaluate side-chains 218 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 279 optimal weight: 40.0000 chunk 417 optimal weight: 30.0000 chunk 441 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 chunk 395 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36963 Z= 0.235 Angle : 0.598 10.919 49842 Z= 0.326 Chirality : 0.061 1.686 5651 Planarity : 0.004 0.098 6415 Dihedral : 10.200 177.295 5242 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.03 (0.11), residues: 4570 helix: -1.02 (0.10), residues: 2066 sheet: -1.27 (0.19), residues: 600 loop : -1.58 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.004 0.001 HIS F 666 PHE 0.021 0.002 PHE L 207 TYR 0.013 0.001 TYR C 611 ARG 0.005 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 4.384 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: C 453 MET cc_start: 0.8396 (tmm) cc_final: 0.7991 (tmm) REVERT: D 504 MET cc_start: 0.6428 (ttp) cc_final: 0.6205 (ttm) REVERT: E 1 MET cc_start: 0.8737 (ttt) cc_final: 0.8451 (tmm) REVERT: E 117 MET cc_start: 0.7930 (mmm) cc_final: 0.7443 (mmm) REVERT: I 219 MET cc_start: 0.9143 (tmm) cc_final: 0.8833 (mmm) outliers start: 2 outliers final: 0 residues processed: 238 average time/residue: 0.9997 time to fit residues: 380.3917 Evaluate side-chains 214 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 367 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 376 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 396 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36963 Z= 0.208 Angle : 0.568 10.931 49842 Z= 0.307 Chirality : 0.061 1.699 5651 Planarity : 0.004 0.056 6415 Dihedral : 9.776 179.815 5242 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 0.10 % Allowed : 1.69 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.79 (0.12), residues: 4570 helix: -0.77 (0.11), residues: 2091 sheet: -1.15 (0.19), residues: 606 loop : -1.53 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS E 323 PHE 0.029 0.002 PHE D 589 TYR 0.013 0.001 TYR F 593 ARG 0.007 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 5.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 453 MET cc_start: 0.8233 (tmm) cc_final: 0.7855 (tmm) REVERT: E 117 MET cc_start: 0.7911 (mmm) cc_final: 0.7414 (mmm) REVERT: H 163 MET cc_start: 0.9145 (ptp) cc_final: 0.8936 (ptp) REVERT: J 46 MET cc_start: 0.9191 (tpt) cc_final: 0.8849 (mtp) REVERT: L 218 MET cc_start: 0.8076 (tpp) cc_final: 0.7758 (mpp) outliers start: 4 outliers final: 1 residues processed: 235 average time/residue: 0.9765 time to fit residues: 371.4960 Evaluate side-chains 214 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 4.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 148 optimal weight: 8.9990 chunk 397 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 442 optimal weight: 20.0000 chunk 367 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36963 Z= 0.241 Angle : 0.583 11.134 49842 Z= 0.318 Chirality : 0.060 1.703 5651 Planarity : 0.004 0.055 6415 Dihedral : 9.570 179.272 5242 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.74 % Favored : 93.24 % Rotamer: Outliers : 0.03 % Allowed : 1.18 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.78 (0.12), residues: 4570 helix: -0.73 (0.11), residues: 2093 sheet: -1.17 (0.19), residues: 604 loop : -1.55 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 213 HIS 0.005 0.001 HIS E 323 PHE 0.018 0.002 PHE L 207 TYR 0.012 0.002 TYR F 502 ARG 0.005 0.001 ARG B 725 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 4.319 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: B 248 MET cc_start: 0.7736 (ptp) cc_final: 0.7470 (ptp) REVERT: C 453 MET cc_start: 0.8308 (tmm) cc_final: 0.7756 (tmm) REVERT: D 155 MET cc_start: 0.7695 (pmm) cc_final: 0.7481 (pmm) REVERT: F 372 MET cc_start: 0.1164 (ptt) cc_final: 0.0862 (ptt) REVERT: H 167 MET cc_start: 0.9252 (tmm) cc_final: 0.9007 (tmm) REVERT: L 218 MET cc_start: 0.8031 (tpp) cc_final: 0.7655 (mpp) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 1.0056 time to fit residues: 364.2593 Evaluate side-chains 205 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 250 optimal weight: 0.5980 chunk 372 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 440 optimal weight: 2.9990 chunk 275 optimal weight: 50.0000 chunk 268 optimal weight: 10.0000 chunk 203 optimal weight: 30.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36963 Z= 0.205 Angle : 0.560 10.960 49842 Z= 0.302 Chirality : 0.061 1.703 5651 Planarity : 0.004 0.051 6415 Dihedral : 9.255 179.366 5242 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.74 % Favored : 93.24 % Rotamer: Outliers : 0.03 % Allowed : 0.97 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.59 (0.12), residues: 4570 helix: -0.55 (0.11), residues: 2099 sheet: -1.07 (0.20), residues: 615 loop : -1.50 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 213 HIS 0.007 0.001 HIS D 323 PHE 0.016 0.001 PHE E 235 TYR 0.019 0.001 TYR L 200 ARG 0.006 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 4.557 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: D 155 MET cc_start: 0.7855 (pmm) cc_final: 0.7627 (pmm) REVERT: F 372 MET cc_start: 0.1818 (ptt) cc_final: 0.1596 (ptt) REVERT: L 218 MET cc_start: 0.7834 (tpp) cc_final: 0.7503 (mpp) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.9830 time to fit residues: 348.0652 Evaluate side-chains 206 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 272 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 263 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 280 optimal weight: 20.0000 chunk 300 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 346 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36963 Z= 0.229 Angle : 0.569 11.000 49842 Z= 0.309 Chirality : 0.061 1.716 5651 Planarity : 0.004 0.064 6415 Dihedral : 9.180 179.035 5242 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.18 % Favored : 92.80 % Rotamer: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.53 (0.12), residues: 4570 helix: -0.52 (0.11), residues: 2094 sheet: -1.11 (0.20), residues: 612 loop : -1.42 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 213 HIS 0.005 0.001 HIS K 213 PHE 0.015 0.002 PHE D 235 TYR 0.011 0.001 TYR F 502 ARG 0.006 0.001 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8385 (pmm) cc_final: 0.7804 (pmm) REVERT: D 155 MET cc_start: 0.7851 (pmm) cc_final: 0.7617 (pmm) REVERT: E 117 MET cc_start: 0.7835 (mmm) cc_final: 0.7369 (mmm) REVERT: F 372 MET cc_start: 0.2117 (ptt) cc_final: 0.1784 (ptt) REVERT: F 655 MET cc_start: 0.6827 (tpt) cc_final: 0.6600 (tpt) REVERT: L 218 MET cc_start: 0.7909 (tpp) cc_final: 0.7577 (mpp) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.9716 time to fit residues: 344.9956 Evaluate side-chains 205 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 400 optimal weight: 20.0000 chunk 421 optimal weight: 0.0050 chunk 385 optimal weight: 20.0000 chunk 410 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 chunk 125 optimal weight: 30.0000 chunk 370 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 409 optimal weight: 9.9990 overall best weight: 7.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36963 Z= 0.266 Angle : 0.610 10.958 49842 Z= 0.333 Chirality : 0.061 1.725 5651 Planarity : 0.004 0.053 6415 Dihedral : 9.239 177.102 5242 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.88 % Favored : 92.10 % Rotamer: Outliers : 0.03 % Allowed : 0.49 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.73 (0.12), residues: 4570 helix: -0.72 (0.11), residues: 2102 sheet: -1.24 (0.20), residues: 612 loop : -1.45 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 213 HIS 0.008 0.001 HIS D 323 PHE 0.020 0.002 PHE F 562 TYR 0.043 0.002 TYR F 593 ARG 0.008 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 4.368 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: A 340 MET cc_start: 0.8411 (pmm) cc_final: 0.7976 (pmm) REVERT: C 453 MET cc_start: 0.8105 (tmm) cc_final: 0.7838 (tmm) REVERT: D 155 MET cc_start: 0.7776 (pmm) cc_final: 0.7520 (pmm) REVERT: E 117 MET cc_start: 0.7750 (mmm) cc_final: 0.7276 (mmm) REVERT: F 372 MET cc_start: 0.2233 (ptt) cc_final: 0.1926 (ptt) REVERT: L 218 MET cc_start: 0.8086 (tpp) cc_final: 0.7765 (mpp) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.9727 time to fit residues: 343.3426 Evaluate side-chains 203 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 269 optimal weight: 6.9990 chunk 434 optimal weight: 9.9990 chunk 264 optimal weight: 0.0770 chunk 205 optimal weight: 30.0000 chunk 301 optimal weight: 4.9990 chunk 455 optimal weight: 20.0000 chunk 419 optimal weight: 20.0000 chunk 362 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 280 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 overall best weight: 6.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 ASN D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36963 Z= 0.238 Angle : 0.584 10.978 49842 Z= 0.316 Chirality : 0.061 1.716 5651 Planarity : 0.004 0.054 6415 Dihedral : 9.166 178.558 5242 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 4570 helix: -0.65 (0.11), residues: 2093 sheet: -1.20 (0.20), residues: 610 loop : -1.43 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 213 HIS 0.007 0.001 HIS D 323 PHE 0.016 0.002 PHE D 235 TYR 0.041 0.002 TYR F 593 ARG 0.006 0.001 ARG H 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 5.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8406 (pmm) cc_final: 0.7980 (pmm) REVERT: B 248 MET cc_start: 0.7756 (ptp) cc_final: 0.7458 (ptp) REVERT: C 453 MET cc_start: 0.8085 (tmm) cc_final: 0.7829 (tmm) REVERT: D 155 MET cc_start: 0.7838 (pmm) cc_final: 0.7587 (pmm) REVERT: E 117 MET cc_start: 0.7679 (mmm) cc_final: 0.7188 (mmm) REVERT: F 372 MET cc_start: 0.2359 (ptt) cc_final: 0.2045 (ptt) REVERT: F 655 MET cc_start: 0.6967 (tpt) cc_final: 0.6621 (tpt) REVERT: L 218 MET cc_start: 0.8060 (tpp) cc_final: 0.7747 (mpp) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.9778 time to fit residues: 350.4385 Evaluate side-chains 201 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 287 optimal weight: 20.0000 chunk 386 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 334 optimal weight: 0.0000 chunk 53 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 363 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 372 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 ASN E 685 ASN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.035138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.021863 restraints weight = 1321689.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.022530 restraints weight = 722244.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.023130 restraints weight = 456839.355| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36963 Z= 0.179 Angle : 0.550 11.077 49842 Z= 0.292 Chirality : 0.061 1.703 5651 Planarity : 0.004 0.053 6415 Dihedral : 8.948 177.280 5242 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.05 % Favored : 92.93 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.29 (0.12), residues: 4570 helix: -0.31 (0.11), residues: 2073 sheet: -1.02 (0.20), residues: 607 loop : -1.29 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 213 HIS 0.005 0.001 HIS L 79 PHE 0.015 0.001 PHE E 235 TYR 0.033 0.001 TYR F 593 ARG 0.014 0.001 ARG J 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9563.81 seconds wall clock time: 169 minutes 24.18 seconds (10164.18 seconds total)