Starting phenix.real_space_refine (version: dev) on Fri Dec 16 06:44:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/12_2022/6w6j_21557_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/12_2022/6w6j_21557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/12_2022/6w6j_21557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/12_2022/6w6j_21557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/12_2022/6w6j_21557_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/12_2022/6w6j_21557_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 197": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C GLU 729": "OE1" <-> "OE2" Residue "D ASP 69": "OD1" <-> "OD2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ASP 346": "OD1" <-> "OD2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ASP 536": "OD1" <-> "OD2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D ASP 584": "OD1" <-> "OD2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 679": "OD1" <-> "OD2" Residue "D ASP 710": "OD1" <-> "OD2" Residue "D PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ARG 588": "NH1" <-> "NH2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E ARG 775": "NH1" <-> "NH2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F GLU 424": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "F GLU 531": "OE1" <-> "OE2" Residue "F ARG 552": "NH1" <-> "NH2" Residue "F GLU 555": "OE1" <-> "OE2" Residue "F PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 628": "OE1" <-> "OE2" Residue "F GLU 641": "OE1" <-> "OE2" Residue "F ARG 669": "NH1" <-> "NH2" Residue "F GLU 680": "OE1" <-> "OE2" Residue "F GLU 759": "OE1" <-> "OE2" Residue "F ARG 796": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 29240 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4796 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 24, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4804 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 24, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4821 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 5393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5393 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 34, 'TRANS': 672} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4702 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} 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: {'AGS': 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: {'AGS': 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: {'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.91, per 1000 atoms: 0.54 Number of scatterers: 29240 At special positions: 0 Unit cell: (137.472, 146.064, 138.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 34 15.00 O 5677 8.00 N 5326 7.00 C 18133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.25 Conformation dependent library (CDL) restraints added in 4.6 seconds 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6902 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 23 sheets defined 46.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.669A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.274A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.885A pdb=" N ALA A 328 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 329 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 331 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 removed outlier: 5.647A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.159A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.941A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.512A pdb=" N ARG A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 468 removed outlier: 3.586A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 557 through 560 No H-bonds generated for 'chain 'A' and resid 557 through 560' Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.878A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 590 removed outlier: 3.955A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 625 removed outlier: 3.539A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 Processing helix chain 'A' and resid 665 through 668 No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 692 through 695 No H-bonds generated for 'chain 'A' and resid 692 through 695' Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 741 through 744 No H-bonds generated for 'chain 'A' and resid 741 through 744' Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.572A pdb=" N LEU A 761 " --> pdb=" O PRO A 758 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 762 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG A 763 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP A 766 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 805 through 823 removed outlier: 4.437A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 242 through 245 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.628A pdb=" N ALA B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 4.124A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 344 through 361 removed outlier: 3.531A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.528A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 407 removed outlier: 5.015A pdb=" N ASP B 393 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 removed outlier: 3.508A pdb=" N ARG B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 468 removed outlier: 3.667A pdb=" N GLU B 440 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 441 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 443 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 445 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG B 446 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 453 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 456 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 460 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP B 463 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 465 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN B 468 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.937A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 590 removed outlier: 3.746A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 625 removed outlier: 3.956A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 645 Processing helix chain 'B' and resid 665 through 668 No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 688 through 695 removed outlier: 4.740A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL B 695 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 735 No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 741 through 744 No H-bonds generated for 'chain 'B' and resid 741 through 744' Processing helix chain 'B' and resid 759 through 779 removed outlier: 4.742A pdb=" N ARG B 763 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 765 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 778 " --> pdb=" O ARG B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.730A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 823 removed outlier: 3.669A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.662A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.932A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 305' Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.715A pdb=" N ARG C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 333' Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.561A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 368 through 380 removed outlier: 4.086A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 392 through 406 Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.800A pdb=" N ALA C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 468 removed outlier: 3.574A pdb=" N ARG C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 558 through 570 removed outlier: 5.668A pdb=" N GLU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 590 removed outlier: 4.056A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 642 through 648 removed outlier: 3.517A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 647 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing helix chain 'C' and resid 693 through 697 Processing helix chain 'C' and resid 730 through 738 removed outlier: 3.841A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 746 removed outlier: 4.108A pdb=" N ARG C 746 " --> pdb=" O GLU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 4.301A pdb=" N GLN C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 796 removed outlier: 3.819A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 823 removed outlier: 5.269A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 22 Processing helix chain 'D' and resid 31 through 39 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 133 through 136 No H-bonds generated for 'chain 'D' and resid 133 through 136' Processing helix chain 'D' and resid 141 through 144 No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 160 through 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 212 through 224 removed outlier: 4.032A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 280 through 283 removed outlier: 3.584A pdb=" N ILE D 283 " --> pdb=" O LEU D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.978A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 322 Processing helix chain 'D' and resid 328 through 333 removed outlier: 4.555A pdb=" N ARG D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 361 removed outlier: 5.400A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 380 removed outlier: 3.884A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 406 removed outlier: 4.153A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 544 removed outlier: 3.755A pdb=" N ALA D 539 " --> pdb=" O PRO D 535 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 562 Processing helix chain 'D' and resid 564 through 570 removed outlier: 3.633A pdb=" N LYS D 570 " --> pdb=" O ASP D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.554A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.555A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 689 through 695 removed outlier: 4.444A pdb=" N GLN D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 738 Processing helix chain 'D' and resid 741 through 744 No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 758 through 777 removed outlier: 4.240A pdb=" N LEU D 761 " --> pdb=" O PRO D 758 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL D 762 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG D 763 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 777 " --> pdb=" O LYS D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 808 through 822 removed outlier: 6.123A pdb=" N ASP D 817 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLN D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 185 through 195 removed outlier: 3.790A pdb=" N SER E 195 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 255 through 268 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.037A pdb=" N ARG E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 323 Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 344 through 353 removed outlier: 3.778A pdb=" N GLY E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 387 through 406 removed outlier: 3.935A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 546 removed outlier: 4.588A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 563 removed outlier: 4.340A pdb=" N ARG E 563 " --> pdb=" O ALA E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 589 Processing helix chain 'E' and resid 613 through 624 removed outlier: 4.236A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 648 removed outlier: 3.771A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 683 No H-bonds generated for 'chain 'E' and resid 681 through 683' Processing helix chain 'E' and resid 688 through 697 Processing helix chain 'E' and resid 730 through 738 Processing helix chain 'E' and resid 762 through 777 removed outlier: 4.017A pdb=" N LYS E 774 " --> pdb=" O ALA E 770 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG E 775 " --> pdb=" O GLN E 771 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU E 776 " --> pdb=" O LEU E 772 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA E 777 " --> pdb=" O GLY E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 797 removed outlier: 4.139A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 807 No H-bonds generated for 'chain 'E' and resid 805 through 807' Processing helix chain 'E' and resid 809 through 819 removed outlier: 3.605A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 825 No H-bonds generated for 'chain 'E' and resid 822 through 825' Processing helix chain 'F' and resid 170 through 174 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 256 through 268 removed outlier: 4.162A pdb=" N LYS F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 302 through 305 No H-bonds generated for 'chain 'F' and resid 302 through 305' Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 331 through 333 No H-bonds generated for 'chain 'F' and resid 331 through 333' Processing helix chain 'F' and resid 344 through 358 removed outlier: 4.010A pdb=" N GLY F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 356 " --> pdb=" O ARG F 352 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG F 357 " --> pdb=" O GLY F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 381 removed outlier: 3.872A pdb=" N SER F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASP F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG F 380 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 406 removed outlier: 4.957A pdb=" N ILE F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 427 Processing helix chain 'F' and resid 439 through 468 removed outlier: 3.674A pdb=" N LYS F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN F 464 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN F 465 " --> pdb=" O THR F 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 466 " --> pdb=" O ARG F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 558 through 570 removed outlier: 4.083A pdb=" N LEU F 562 " --> pdb=" O THR F 558 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS F 570 " --> pdb=" O ASP F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 583 Processing helix chain 'F' and resid 587 through 590 No H-bonds generated for 'chain 'F' and resid 587 through 590' Processing helix chain 'F' and resid 615 through 625 removed outlier: 3.636A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 625 " --> pdb=" O ALA F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 642 through 647 removed outlier: 4.040A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 668 No H-bonds generated for 'chain 'F' and resid 665 through 668' Processing helix chain 'F' and resid 681 through 683 No H-bonds generated for 'chain 'F' and resid 681 through 683' Processing helix chain 'F' and resid 688 through 698 removed outlier: 3.971A pdb=" N LEU F 693 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU F 696 " --> pdb=" O LEU F 693 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP F 697 " --> pdb=" O GLN F 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU F 698 " --> pdb=" O VAL F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 738 Processing helix chain 'F' and resid 758 through 760 No H-bonds generated for 'chain 'F' and resid 758 through 760' Processing helix chain 'F' and resid 762 through 777 Processing helix chain 'F' and resid 787 through 796 Processing helix chain 'F' and resid 805 through 823 removed outlier: 4.541A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 335 through 338 removed outlier: 7.095A pdb=" N GLY A 313 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLY A 206 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 315 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.523A pdb=" N LEU A 716 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 632 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASP A 679 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 634 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 700 through 702 Processing sheet with id= D, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.676A pdb=" N THR B 166 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 312 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 315 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN B 335 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE B 205 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL B 337 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 601 through 604 removed outlier: 3.611A pdb=" N LEU B 718 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASP B 679 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 700 through 702 Processing sheet with id= G, first strand: chain 'B' and resid 782 through 784 removed outlier: 3.559A pdb=" N VAL B 834 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 335 through 338 removed outlier: 6.796A pdb=" N GLY C 313 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 601 through 603 removed outlier: 3.508A pdb=" N PHE C 603 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL C 632 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP C 679 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 634 " --> pdb=" O ASP C 679 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 700 through 702 removed outlier: 3.510A pdb=" N LEU C 701 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 783 through 785 removed outlier: 7.443A pdb=" N VAL C 834 " --> pdb=" O GLN C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 165 through 167 Processing sheet with id= M, first strand: chain 'D' and resid 335 through 338 removed outlier: 6.846A pdb=" N GLY D 313 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLY D 206 " --> pdb=" O GLY D 313 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR D 315 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 314 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 604 through 606 Processing sheet with id= O, first strand: chain 'D' and resid 632 through 635 removed outlier: 6.287A pdb=" N ILE D 715 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE D 678 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE D 717 " --> pdb=" O PHE D 678 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 700 through 702 removed outlier: 3.548A pdb=" N LEU D 701 " --> pdb=" O VAL D 709 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 782 through 784 Processing sheet with id= R, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= S, first strand: chain 'E' and resid 237 through 240 removed outlier: 6.958A pdb=" N ILE E 274 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU E 240 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE E 276 " --> pdb=" O LEU E 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 601 through 604 removed outlier: 3.958A pdb=" N PHE E 603 " --> pdb=" O LEU E 716 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 718 " --> pdb=" O PHE E 603 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 336 through 338 removed outlier: 6.302A pdb=" N VAL F 203 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY F 313 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLY F 206 " --> pdb=" O GLY F 313 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR F 315 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA F 314 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 601 through 606 removed outlier: 3.539A pdb=" N LEU F 718 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER F 720 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR F 719 " --> pdb=" O PHE F 678 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE F 634 " --> pdb=" O ASP F 679 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 700 through 702 928 hydrogen bonds defined for protein. 2505 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: 10.40 Time building geometry restraints manager: 13.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 10418 1.36 - 1.51: 9067 1.51 - 1.66: 10020 1.66 - 1.80: 116 1.80 - 1.95: 14 Bond restraints: 29635 Sorted by residual: bond pdb=" C4 ADP F 902 " pdb=" C5 ADP F 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" CA GLU C 760 " pdb=" C GLU C 760 " ideal model delta sigma weight residual 1.523 1.464 0.058 1.41e-02 5.03e+03 1.70e+01 bond pdb=" C5 ADP F 902 " pdb=" C6 ADP F 902 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C5 ADP E 902 " pdb=" C6 ADP E 902 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 29630 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.90: 676 105.90 - 112.99: 16300 112.99 - 120.09: 11094 120.09 - 127.18: 11743 127.18 - 134.27: 282 Bond angle restraints: 40095 Sorted by residual: angle pdb=" N ILE F 413 " pdb=" CA ILE F 413 " pdb=" C ILE F 413 " ideal model delta sigma weight residual 113.53 105.07 8.46 9.80e-01 1.04e+00 7.44e+01 angle pdb=" N VAL E 801 " pdb=" CA VAL E 801 " pdb=" C VAL E 801 " ideal model delta sigma weight residual 113.53 106.18 7.35 9.80e-01 1.04e+00 5.62e+01 angle pdb=" N VAL B 801 " pdb=" CA VAL B 801 " pdb=" C VAL B 801 " ideal model delta sigma weight residual 113.71 107.37 6.34 9.50e-01 1.11e+00 4.45e+01 angle pdb=" N ILE C 413 " pdb=" CA ILE C 413 " pdb=" C ILE C 413 " ideal model delta sigma weight residual 112.12 106.89 5.23 8.40e-01 1.42e+00 3.87e+01 angle pdb=" N VAL C 246 " pdb=" CA VAL C 246 " pdb=" C VAL C 246 " ideal model delta sigma weight residual 111.91 107.37 4.54 8.90e-01 1.26e+00 2.61e+01 ... (remaining 40090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.96: 17634 31.96 - 63.91: 527 63.91 - 95.87: 41 95.87 - 127.83: 4 127.83 - 159.78: 1 Dihedral angle restraints: 18207 sinusoidal: 7511 harmonic: 10696 Sorted by residual: dihedral pdb=" CA LEU B 387 " pdb=" C LEU B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual 180.00 -117.78 -62.22 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA PHE C 386 " pdb=" C PHE C 386 " pdb=" N LEU C 387 " pdb=" CA LEU C 387 " ideal model delta harmonic sigma weight residual -180.00 -141.16 -38.84 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA PHE D 386 " pdb=" C PHE D 386 " pdb=" N LEU D 387 " pdb=" CA LEU D 387 " ideal model delta harmonic sigma weight residual 180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 ... (remaining 18204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3881 0.068 - 0.135: 658 0.135 - 0.203: 52 0.203 - 0.270: 4 0.270 - 0.338: 1 Chirality restraints: 4596 Sorted by residual: chirality pdb=" CB ILE D 681 " pdb=" CA ILE D 681 " pdb=" CG1 ILE D 681 " pdb=" CG2 ILE D 681 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB VAL D 246 " pdb=" CA VAL D 246 " pdb=" CG1 VAL D 246 " pdb=" CG2 VAL D 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE D 29 " pdb=" CA ILE D 29 " pdb=" CG1 ILE D 29 " pdb=" CG2 ILE D 29 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4593 not shown) Planarity restraints: 5253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 273 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C ILE D 273 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE D 273 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE D 274 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " 0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO B 388 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 812 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C GLN D 812 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN D 812 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN D 813 " 0.017 2.00e-02 2.50e+03 ... (remaining 5250 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 22 2.15 - 2.84: 10043 2.84 - 3.52: 39056 3.52 - 4.21: 63742 4.21 - 4.90: 111540 Nonbonded interactions: 224403 Sorted by model distance: nonbonded pdb=" NZ LYS D 250 " pdb=" N GLU E 254 " model vdw 1.459 3.200 nonbonded pdb=" NZ LYS D 250 " pdb=" CA GLY E 253 " model vdw 1.475 3.520 nonbonded pdb=" NZ LYS D 250 " pdb=" C GLY E 253 " model vdw 1.616 3.350 nonbonded pdb=" OE2 GLU C 426 " pdb=" NH1 ARG D 352 " model vdw 1.709 2.520 nonbonded pdb=" OG1 THR E 614 " pdb=" O1A ADP E 902 " model vdw 1.813 2.440 ... (remaining 224398 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 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'B' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'C' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 845 or resid 901)) selection = (chain 'F' and (resid 159 through 407 or resid 530 through 845 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 70 5.16 5 C 18133 2.51 5 N 5326 2.21 5 O 5677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.210 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: 0.030 Extract box with map and model: 12.680 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.260 Process input model: 74.180 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.007 0.109 29635 Z= 0.460 Angle : 0.888 13.970 40095 Z= 0.494 Chirality : 0.050 0.338 4596 Planarity : 0.005 0.095 5253 Dihedral : 15.315 159.781 11305 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.36 % Favored : 87.48 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -4.72 (0.11), residues: 3681 helix: -2.70 (0.09), residues: 1835 sheet: -2.99 (0.24), residues: 359 loop : -3.60 (0.13), residues: 1487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 444 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 23 residues processed: 468 average time/residue: 0.5325 time to fit residues: 357.6119 Evaluate side-chains 233 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 3.320 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 23 average time/residue: 0.2259 time to fit residues: 14.5863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 337 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 268 ASN A 323 HIS B 335 GLN B 361 HIS B 452 GLN B 643 HIS B 685 HIS B 812 GLN C 323 HIS C 335 GLN C 361 HIS C 575 GLN C 643 HIS C 663 GLN D 11 GLN D 95 GLN D 129 HIS D 335 GLN D 643 HIS D 705 HIS E 201 ASN E 685 HIS ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 29635 Z= 0.199 Angle : 0.659 14.660 40095 Z= 0.326 Chirality : 0.043 0.182 4596 Planarity : 0.005 0.092 5253 Dihedral : 8.546 144.004 4241 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.16 % Favored : 90.74 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.06 % 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: -3.31 (0.13), residues: 3681 helix: -1.41 (0.11), residues: 1826 sheet: -2.61 (0.23), residues: 392 loop : -3.02 (0.14), residues: 1463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 227 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 39 residues processed: 279 average time/residue: 0.4637 time to fit residues: 200.0191 Evaluate side-chains 214 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 3.830 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 22 residues processed: 39 average time/residue: 0.2679 time to fit residues: 24.5267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 281 optimal weight: 0.2980 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 338 optimal weight: 20.0000 chunk 365 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 271 optimal weight: 0.6980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 29635 Z= 0.320 Angle : 0.687 14.217 40095 Z= 0.336 Chirality : 0.045 0.219 4596 Planarity : 0.005 0.101 5253 Dihedral : 8.392 141.573 4241 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.27 % Favored : 89.60 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % 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: -2.67 (0.13), residues: 3681 helix: -0.93 (0.12), residues: 1822 sheet: -2.27 (0.24), residues: 388 loop : -2.65 (0.15), residues: 1471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 193 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 57 residues processed: 277 average time/residue: 0.4181 time to fit residues: 186.7978 Evaluate side-chains 221 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 164 time to evaluate : 3.626 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 23 residues processed: 57 average time/residue: 0.2480 time to fit residues: 31.6203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.0270 chunk 254 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 161 optimal weight: 0.0010 chunk 227 optimal weight: 0.0370 chunk 339 optimal weight: 0.0010 chunk 359 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 321 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 overall best weight: 0.1728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 705 HIS B 201 ASN C 829 HIS F 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.082 29635 Z= 0.141 Angle : 0.580 13.674 40095 Z= 0.283 Chirality : 0.041 0.189 4596 Planarity : 0.004 0.089 5253 Dihedral : 7.947 141.617 4241 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.96 % Favored : 90.95 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.14), residues: 3681 helix: -0.54 (0.13), residues: 1820 sheet: -1.91 (0.25), residues: 379 loop : -2.36 (0.15), residues: 1482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 32 residues processed: 256 average time/residue: 0.3987 time to fit residues: 166.7854 Evaluate side-chains 199 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 3.774 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 32 average time/residue: 0.2654 time to fit residues: 20.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 0.1980 chunk 306 optimal weight: 0.0270 chunk 248 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 322 optimal weight: 0.7980 chunk 90 optimal weight: 0.0020 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS E 201 ASN F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.085 29635 Z= 0.137 Angle : 0.569 13.387 40095 Z= 0.275 Chirality : 0.041 0.258 4596 Planarity : 0.004 0.083 5253 Dihedral : 7.729 140.530 4241 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.42 % Favored : 91.47 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3681 helix: -0.25 (0.13), residues: 1805 sheet: -1.79 (0.25), residues: 388 loop : -2.15 (0.16), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 178 time to evaluate : 3.405 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 32 residues processed: 223 average time/residue: 0.4017 time to fit residues: 146.2189 Evaluate side-chains 191 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 3.852 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 32 average time/residue: 0.2571 time to fit residues: 20.9217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.8980 chunk 323 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 359 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN F 201 ASN F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 29635 Z= 0.169 Angle : 0.575 13.314 40095 Z= 0.276 Chirality : 0.041 0.241 4596 Planarity : 0.004 0.088 5253 Dihedral : 7.653 139.727 4241 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.05 % Favored : 90.84 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3681 helix: -0.08 (0.13), residues: 1800 sheet: -1.75 (0.25), residues: 398 loop : -2.03 (0.16), residues: 1483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 3.618 Fit side-chains outliers start: 53 outliers final: 36 residues processed: 217 average time/residue: 0.4000 time to fit residues: 142.8788 Evaluate side-chains 194 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 23 residues processed: 36 average time/residue: 0.2496 time to fit residues: 22.1501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 302 optimal weight: 0.0470 chunk 200 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 29635 Z= 0.230 Angle : 0.620 13.318 40095 Z= 0.297 Chirality : 0.043 0.333 4596 Planarity : 0.005 0.094 5253 Dihedral : 7.725 139.363 4241 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.37 % Favored : 90.52 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3681 helix: -0.00 (0.13), residues: 1816 sheet: -1.61 (0.25), residues: 391 loop : -2.07 (0.16), residues: 1474 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 3.953 Fit side-chains outliers start: 44 outliers final: 31 residues processed: 207 average time/residue: 0.4025 time to fit residues: 137.5816 Evaluate side-chains 190 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 3.838 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 31 average time/residue: 0.2673 time to fit residues: 21.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 214 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 281 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 GLN F 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.081 29635 Z= 0.146 Angle : 0.575 12.561 40095 Z= 0.276 Chirality : 0.041 0.249 4596 Planarity : 0.004 0.088 5253 Dihedral : 7.550 136.112 4241 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.06 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3681 helix: 0.15 (0.13), residues: 1804 sheet: -1.55 (0.25), residues: 393 loop : -1.93 (0.16), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 28 residues processed: 206 average time/residue: 0.4136 time to fit residues: 139.6540 Evaluate side-chains 178 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 3.576 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 28 average time/residue: 0.2531 time to fit residues: 18.3508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 8.9990 chunk 343 optimal weight: 5.9990 chunk 313 optimal weight: 0.0010 chunk 334 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 102 optimal weight: 0.0030 chunk 301 optimal weight: 10.0000 chunk 316 optimal weight: 0.7980 chunk 332 optimal weight: 5.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 29635 Z= 0.211 Angle : 0.603 12.278 40095 Z= 0.288 Chirality : 0.042 0.246 4596 Planarity : 0.004 0.093 5253 Dihedral : 7.587 135.194 4241 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.13 % Favored : 90.79 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3681 helix: 0.19 (0.13), residues: 1816 sheet: -1.50 (0.25), residues: 402 loop : -1.93 (0.16), residues: 1463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 3.942 Fit side-chains outliers start: 39 outliers final: 34 residues processed: 192 average time/residue: 0.4077 time to fit residues: 129.8127 Evaluate side-chains 182 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 3.786 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 24 residues processed: 34 average time/residue: 0.2547 time to fit residues: 21.4045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 167 optimal weight: 0.2980 chunk 245 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 chunk 341 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 29635 Z= 0.168 Angle : 0.585 12.548 40095 Z= 0.279 Chirality : 0.042 0.284 4596 Planarity : 0.004 0.091 5253 Dihedral : 7.518 133.417 4241 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.07 % Favored : 90.84 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3681 helix: 0.30 (0.13), residues: 1809 sheet: -1.50 (0.25), residues: 387 loop : -1.87 (0.16), residues: 1485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 4.128 Fit side-chains outliers start: 34 outliers final: 27 residues processed: 194 average time/residue: 0.4351 time to fit residues: 139.4724 Evaluate side-chains 180 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 27 average time/residue: 0.2625 time to fit residues: 18.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.7980 chunk 314 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 295 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 303 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.0170 overall best weight: 0.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.088569 restraints weight = 55617.874| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.10 r_work: 0.2981 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.079 29635 Z= 0.138 Angle : 0.572 12.131 40095 Z= 0.273 Chirality : 0.041 0.248 4596 Planarity : 0.004 0.087 5253 Dihedral : 7.407 131.757 4241 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.23 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3681 helix: 0.40 (0.13), residues: 1822 sheet: -1.40 (0.26), residues: 384 loop : -1.76 (0.17), residues: 1475 =============================================================================== Job complete usr+sys time: 5223.98 seconds wall clock time: 96 minutes 2.25 seconds (5762.25 seconds total)