Starting phenix.real_space_refine on Sat Aug 10 13:58:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/08_2024/6w6j_21557_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/08_2024/6w6j_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_21557/08_2024/6w6j_21557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/08_2024/6w6j_21557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/08_2024/6w6j_21557_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6j_21557/08_2024/6w6j_21557_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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-5409/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: 16.52, per 1000 atoms: 0.56 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: 11.87 Conformation dependent library (CDL) restraints added in 5.3 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... Secondary structure from input PDB file: 193 helices and 28 sheets defined 54.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 168 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 183 through 195 removed outlier: 3.631A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.858A pdb=" N VAL A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.621A pdb=" N ARG A 233 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.729A pdb=" N SER A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 317 through 324 removed outlier: 4.274A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.691A pdb=" N GLU A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 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 367 through 377 removed outlier: 3.604A pdb=" N LEU A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 391 through 407 removed outlier: 4.272A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 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 438 through 469 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 535 through 545 removed outlier: 3.932A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.811A pdb=" N LYS A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 575 through 591 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 614 through 626 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 641 through 648 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.711A pdb=" N ALA A 667 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 687 through 690 Processing helix chain 'A' and resid 691 through 696 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.919A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 757 through 760 Processing helix chain 'A' and resid 761 through 776 removed outlier: 3.914A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 797 removed outlier: 3.943A pdb=" N GLY A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 824 removed outlier: 3.776A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) 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 174 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.517A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.991A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.577A pdb=" N VAL B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 3.602A pdb=" N SER B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.815A pdb=" N VAL B 284 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 removed outlier: 4.789A pdb=" N MET B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) 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) removed outlier: 3.576A pdb=" N GLY B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.665A pdb=" N TYR B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) 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 330 through 334 removed outlier: 3.716A pdb=" N PHE B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 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 367 through 377 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) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.609A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 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 438 through 469 removed outlier: 4.475A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 563 removed outlier: 3.746A pdb=" N LYS B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.937A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.989A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) 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 615 through 626 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 641 through 648 removed outlier: 3.644A pdb=" N ALA B 646 " --> pdb=" O HIS B 643 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 647 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.616A pdb=" N LYS B 683 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 693 Processing helix chain 'B' and resid 731 through 736 removed outlier: 3.704A pdb=" N ARG B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 761 through 777 removed outlier: 3.811A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 780 No H-bonds generated for 'chain 'B' and resid 778 through 780' Processing helix chain 'B' and resid 786 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 805 through 824 removed outlier: 3.552A pdb=" N ARG B 809 " --> pdb=" O ARG B 805 " (cutoff:3.500A) 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) removed outlier: 3.516A pdb=" N LEU B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.670A pdb=" N ILE C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.963A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.662A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 300 through 306 removed outlier: 3.932A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 306 " --> pdb=" O PRO C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.715A pdb=" N ARG C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.561A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 367 through 381 removed outlier: 3.609A pdb=" N LEU C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.734A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.800A pdb=" N ALA C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 469 removed outlier: 4.386A pdb=" N GLU C 440 " --> pdb=" O GLU C 436 " (cutoff:3.500A) 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 536 through 545 Processing helix chain 'C' and resid 557 through 569 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) Processing helix chain 'C' and resid 575 through 591 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) removed outlier: 3.530A pdb=" N ALA C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 626 Processing helix chain 'C' and resid 627 through 631 removed outlier: 3.910A pdb=" N MET C 631 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 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 669 Processing helix chain 'C' and resid 680 through 684 removed outlier: 3.682A pdb=" N ALA C 684 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 698 Processing helix chain 'C' and resid 730 through 739 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 740 through 745 Processing helix chain 'C' and resid 757 through 777 removed outlier: 3.864A pdb=" N VAL C 762 " --> pdb=" O PRO C 758 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 780 No H-bonds generated for 'chain 'C' and resid 778 through 780' Processing helix chain 'C' and resid 786 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 805 through 824 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 7 through 23 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.910A pdb=" N LEU D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 53 removed outlier: 3.605A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.527A pdb=" N ASP D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.597A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.707A pdb=" N LYS D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.542A pdb=" N GLU D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.609A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 225 removed outlier: 4.032A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 4.009A pdb=" N ARG D 233 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 4.022A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.584A pdb=" N ILE D 283 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL D 284 " --> pdb=" O HIS D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 284' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 343 through 362 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) removed outlier: 3.532A pdb=" N HIS D 362 " --> pdb=" O TYR D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 removed outlier: 3.687A pdb=" N LEU D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 407 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 534 through 545 removed outlier: 3.792A pdb=" N ILE D 538 " --> pdb=" O GLY D 534 " (cutoff:3.500A) 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 557 through 563 removed outlier: 3.604A pdb=" N ARG D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.687A pdb=" N GLU D 567 " --> pdb=" O ARG D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.554A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 626 Processing helix chain 'D' and resid 637 through 639 No H-bonds generated for 'chain 'D' and resid 637 through 639' Processing helix chain 'D' and resid 642 through 648 removed outlier: 3.665A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.797A pdb=" N ARG D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 4.004A pdb=" N LEU D 692 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 739 Processing helix chain 'D' and resid 740 through 745 Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 776 Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 807 through 815 Processing helix chain 'D' and resid 815 through 821 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 184 through 194 removed outlier: 3.878A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 241 through 245 removed outlier: 3.520A pdb=" N SER E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 316 through 324 Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.763A pdb=" N PHE E 334 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 354 removed outlier: 3.778A pdb=" N GLY E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 386 through 405 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) Processing helix chain 'E' and resid 535 through 547 removed outlier: 4.588A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 575 through 590 Processing helix chain 'E' and resid 612 through 625 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 642 through 649 removed outlier: 3.841A pdb=" N VAL E 645 " --> pdb=" O LYS E 642 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 684 Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.937A pdb=" N VAL E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 739 removed outlier: 4.122A pdb=" N ALA E 733 " --> pdb=" O GLU E 729 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE E 739 " --> pdb=" O VAL E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 773 Processing helix chain 'E' and resid 774 through 778 removed outlier: 4.031A pdb=" N GLN E 778 " --> pdb=" O ARG E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 793 Processing helix chain 'E' and resid 793 through 798 Processing helix chain 'E' and resid 808 through 820 removed outlier: 3.605A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) Processing helix chain 'E' and resid 821 through 826 Processing helix chain 'F' and resid 169 through 175 removed outlier: 3.751A pdb=" N ARG F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 211 through 226 Processing helix chain 'F' and resid 257 through 269 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 283 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.520A pdb=" N ARG F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 325 removed outlier: 3.909A pdb=" N GLU F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 removed outlier: 4.025A pdb=" N PHE F 334 " --> pdb=" O GLU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 359 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 367 through 375 Processing helix chain 'F' and resid 377 through 382 removed outlier: 3.797A pdb=" N TYR F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 407 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) removed outlier: 4.029A pdb=" N ASP F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 428 Processing helix chain 'F' and resid 438 through 469 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 535 through 544 removed outlier: 3.678A pdb=" N ALA F 539 " --> pdb=" O PRO F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 4.002A pdb=" N LEU F 561 " --> pdb=" O GLU F 557 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 562 " --> pdb=" O THR F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 569 through 571 No H-bonds generated for 'chain 'F' and resid 569 through 571' Processing helix chain 'F' and resid 575 through 584 Processing helix chain 'F' and resid 586 through 591 Processing helix chain 'F' and resid 614 through 626 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 627 through 631 removed outlier: 3.651A pdb=" N MET F 631 " --> pdb=" O GLU F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 648 removed outlier: 3.537A pdb=" N THR F 644 " --> pdb=" O GLU F 641 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 648 " --> pdb=" O VAL F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 669 Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 688 through 699 removed outlier: 3.676A pdb=" N GLN F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP F 697 " --> pdb=" O LEU F 693 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 698 " --> pdb=" O GLN F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 739 Processing helix chain 'F' and resid 757 through 760 Processing helix chain 'F' and resid 761 through 776 Processing helix chain 'F' and resid 786 through 797 Processing helix chain 'F' and resid 804 through 824 removed outlier: 3.677A pdb=" N ARG F 808 " --> pdb=" O ALA F 804 " (cutoff:3.500A) 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) removed outlier: 3.911A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 6.492A pdb=" N THR A 275 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ALA A 314 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE A 277 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N THR A 316 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 206 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 7.170A pdb=" N ARG A 365 " --> pdb=" O VAL A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 635 removed outlier: 8.657A pdb=" N LEU A 751 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET A 604 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 702 Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 785 removed outlier: 6.801A pdb=" N GLN A 784 " --> pdb=" O VAL A 836 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, 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: 7.066A pdb=" N THR B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE B 276 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASP B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N VAL B 312 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR B 275 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ALA B 314 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE B 277 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 315 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL B 203 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 635 removed outlier: 6.273A pdb=" N GLY B 601 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU B 718 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE B 603 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 700 through 702 Processing sheet with id=AA9, first strand: chain 'B' and resid 782 through 785 removed outlier: 7.055A pdb=" N GLN B 782 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL B 836 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN B 784 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL B 838 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 167 removed outlier: 6.646A pdb=" N THR C 275 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ALA C 314 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE C 277 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.410A pdb=" N ARG C 365 " --> pdb=" O VAL C 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 602 through 603 removed outlier: 7.099A pdb=" N PHE C 603 " --> pdb=" O LEU C 718 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'C' and resid 783 through 785 removed outlier: 6.155A pdb=" N GLN C 784 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL C 838 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AB7, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.207A pdb=" N VAL D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP D 278 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR D 275 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ALA D 314 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE D 277 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N THR D 316 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 206 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.825A pdb=" N ARG D 365 " --> pdb=" O VAL D 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 632 through 635 removed outlier: 6.159A pdb=" N VAL D 676 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR D 719 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE D 678 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE D 603 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N SER D 720 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE D 605 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing sheet with id=AC1, 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=AC2, first strand: chain 'D' and resid 782 through 784 Processing sheet with id=AC3, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC4, first strand: chain 'E' and resid 237 through 240 Processing sheet with id=AC5, first strand: chain 'E' and resid 602 through 604 removed outlier: 7.722A pdb=" N PHE E 603 " --> pdb=" O LEU E 718 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E 632 " --> pdb=" O LEU E 677 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 701 through 702 Processing sheet with id=AC7, first strand: chain 'F' and resid 276 through 278 removed outlier: 4.317A pdb=" N ALA F 314 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU F 204 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL F 203 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 632 through 635 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) removed outlier: 3.553A pdb=" N THR F 719 " --> pdb=" O PHE F 678 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY F 601 " --> pdb=" O LEU F 716 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU F 718 " --> pdb=" O GLY F 601 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE F 603 " --> pdb=" O LEU F 718 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N SER F 720 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE F 605 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N LEU F 751 " --> pdb=" O ALA F 602 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET F 604 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 700 through 702 Processing sheet with id=AD1, first strand: chain 'F' and resid 783 through 784 1166 hydrogen bonds defined for protein. 3309 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: 11.16 Time building geometry restraints manager: 12.86 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: 17664 31.96 - 63.91: 607 63.91 - 95.87: 41 95.87 - 127.83: 4 127.83 - 159.78: 1 Dihedral angle restraints: 18317 sinusoidal: 7621 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 18314 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: 10034 2.84 - 3.52: 38813 3.52 - 4.21: 63162 4.21 - 4.90: 111420 Nonbonded interactions: 223451 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 3.120 nonbonded pdb=" OG1 THR E 614 " pdb=" O1A ADP E 902 " model vdw 1.813 3.040 ... (remaining 223446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 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: 3.270 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: 1.230 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 79.650 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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= 0.457 Angle : 0.888 13.970 40095 Z= 0.494 Chirality : 0.050 0.338 4596 Planarity : 0.005 0.095 5253 Dihedral : 15.850 159.781 11415 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.36 % Favored : 87.48 % Rotamer: Outliers : 0.82 % Allowed : 9.55 % Favored : 89.63 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 545 HIS 0.008 0.002 HIS D 685 PHE 0.036 0.002 PHE B 798 TYR 0.019 0.002 TYR D 158 ARG 0.006 0.001 ARG D 333 *********************** 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 : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 464 GLN cc_start: 0.7491 (mm110) cc_final: 0.7023 (mm-40) REVERT: B 462 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7163 (ttt180) REVERT: C 455 LYS cc_start: 0.7814 (tppt) cc_final: 0.7209 (ttpt) REVERT: C 458 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 462 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7407 (ttm-80) REVERT: D 133 PRO cc_start: 0.5849 (Cg_exo) cc_final: 0.5639 (Cg_endo) REVERT: D 331 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8000 (tm-30) REVERT: D 404 MET cc_start: 0.8295 (mmm) cc_final: 0.8066 (tpt) REVERT: D 631 MET cc_start: 0.9068 (ptt) cc_final: 0.8825 (ptt) REVERT: E 163 LYS cc_start: 0.8659 (pttm) cc_final: 0.8286 (ptpp) REVERT: E 281 HIS cc_start: 0.6746 (p90) cc_final: 0.6324 (p90) REVERT: E 323 HIS cc_start: 0.7147 (m170) cc_final: 0.6669 (m170) REVERT: E 745 ASN cc_start: 0.9083 (m-40) cc_final: 0.8818 (m-40) REVERT: E 772 LEU cc_start: 0.8353 (pp) cc_final: 0.7959 (mt) REVERT: E 798 PHE cc_start: 0.5356 (t80) cc_final: 0.4768 (t80) REVERT: F 217 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7006 (mt-10) REVERT: F 299 MET cc_start: 0.5978 (ttt) cc_final: 0.4793 (ttt) REVERT: F 325 GLU cc_start: 0.7513 (tp30) cc_final: 0.6301 (tm-30) REVERT: F 385 ARG cc_start: 0.6180 (mtt180) cc_final: 0.5755 (mmt90) REVERT: F 423 LEU cc_start: 0.8108 (mt) cc_final: 0.7657 (tt) REVERT: F 590 ARG cc_start: 0.6020 (mmt-90) cc_final: 0.5474 (tpt170) outliers start: 25 outliers final: 23 residues processed: 468 average time/residue: 0.5571 time to fit residues: 369.5366 Evaluate side-chains 237 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 833 THR Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 0.0060 chunk 190 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 337 optimal weight: 10.0000 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 A 361 HIS B 335 GLN B 361 HIS B 452 GLN B 643 HIS B 685 HIS C 323 HIS C 335 GLN C 361 HIS C 643 HIS C 663 GLN C 685 HIS D 11 GLN D 95 GLN D 129 HIS D 335 GLN D 643 HIS D 705 HIS E 201 ASN E 685 HIS F 685 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1997 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 : 0.681 15.151 40095 Z= 0.340 Chirality : 0.043 0.212 4596 Planarity : 0.005 0.084 5253 Dihedral : 10.597 144.255 4375 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.91 % Favored : 91.04 % Rotamer: Outliers : 1.58 % Allowed : 13.27 % Favored : 85.15 % 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: -3.13 (0.13), residues: 3681 helix: -1.27 (0.11), residues: 1851 sheet: -2.65 (0.24), residues: 386 loop : -2.89 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 545 HIS 0.008 0.001 HIS B 643 PHE 0.032 0.002 PHE F 386 TYR 0.011 0.001 TYR B 655 ARG 0.007 0.001 ARG F 258 *********************** 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 288 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 240 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8749 (mmm) cc_final: 0.8548 (mmm) REVERT: A 322 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8424 (tttm) REVERT: B 444 LYS cc_start: 0.8809 (tppt) cc_final: 0.8197 (mtmm) REVERT: B 462 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7448 (ttt180) REVERT: B 606 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8983 (pp) REVERT: C 455 LYS cc_start: 0.7746 (tppt) cc_final: 0.7163 (ttpt) REVERT: C 458 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 462 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7422 (ttm-80) REVERT: D 112 MET cc_start: 0.7706 (mmm) cc_final: 0.7366 (ttm) REVERT: D 331 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7918 (tm-30) REVERT: D 404 MET cc_start: 0.8484 (mmm) cc_final: 0.8128 (tpt) REVERT: D 631 MET cc_start: 0.9041 (ptt) cc_final: 0.8786 (ptt) REVERT: E 217 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7893 (mt-10) REVERT: E 281 HIS cc_start: 0.6950 (p90) cc_final: 0.6026 (p90) REVERT: E 319 GLU cc_start: 0.7917 (mm-30) cc_final: 0.6636 (mm-30) REVERT: E 323 HIS cc_start: 0.7302 (m170) cc_final: 0.6564 (m170) REVERT: E 628 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7367 (pp20) REVERT: E 772 LEU cc_start: 0.8477 (pp) cc_final: 0.8258 (mt) REVERT: E 798 PHE cc_start: 0.5334 (t80) cc_final: 0.4683 (t80) REVERT: F 163 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6818 (ptpp) REVERT: F 217 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6819 (mt-10) REVERT: F 245 MET cc_start: 0.3511 (ptt) cc_final: 0.2944 (ttp) REVERT: F 325 GLU cc_start: 0.7393 (tp30) cc_final: 0.6144 (tm-30) REVERT: F 385 ARG cc_start: 0.5990 (mtt180) cc_final: 0.5594 (mmt90) REVERT: F 423 LEU cc_start: 0.8388 (mt) cc_final: 0.7585 (tt) REVERT: F 590 ARG cc_start: 0.6242 (mmt-90) cc_final: 0.5498 (tpt170) outliers start: 48 outliers final: 24 residues processed: 278 average time/residue: 0.4738 time to fit residues: 200.0353 Evaluate side-chains 208 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 281 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 365 optimal weight: 8.9990 chunk 301 optimal weight: 1.9990 chunk 335 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN D 11 GLN D 837 ASN E 201 ASN ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29635 Z= 0.301 Angle : 0.679 13.912 40095 Z= 0.335 Chirality : 0.045 0.291 4596 Planarity : 0.005 0.096 5253 Dihedral : 10.217 145.087 4360 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.45 % Favored : 90.44 % Rotamer: Outliers : 2.67 % Allowed : 14.22 % Favored : 83.11 % 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: -2.42 (0.14), residues: 3681 helix: -0.67 (0.12), residues: 1829 sheet: -2.35 (0.24), residues: 400 loop : -2.55 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 545 HIS 0.008 0.001 HIS E 281 PHE 0.026 0.002 PHE D 605 TYR 0.030 0.002 TYR D 105 ARG 0.013 0.001 ARG E 365 *********************** 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 280 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 199 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8512 (tttm) REVERT: A 701 LEU cc_start: 0.9015 (pt) cc_final: 0.8691 (pt) REVERT: B 444 LYS cc_start: 0.8856 (tppt) cc_final: 0.8176 (mtmm) REVERT: B 462 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7172 (ttt180) REVERT: B 603 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8416 (p90) REVERT: B 606 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9184 (pp) REVERT: B 783 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8731 (pp) REVERT: C 455 LYS cc_start: 0.7814 (tppt) cc_final: 0.7236 (ttpt) REVERT: C 462 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7362 (ttm-80) REVERT: D 112 MET cc_start: 0.7611 (mmm) cc_final: 0.7294 (ttm) REVERT: D 250 LYS cc_start: 0.8737 (pptt) cc_final: 0.8489 (pptt) REVERT: D 331 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 404 MET cc_start: 0.8550 (mmm) cc_final: 0.8199 (tpt) REVERT: E 281 HIS cc_start: 0.6770 (p90) cc_final: 0.6267 (p-80) REVERT: E 628 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7384 (pp20) REVERT: E 772 LEU cc_start: 0.8460 (pp) cc_final: 0.8224 (mt) REVERT: E 798 PHE cc_start: 0.5542 (t80) cc_final: 0.4806 (t80) REVERT: F 217 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6799 (mt-10) REVERT: F 240 LEU cc_start: 0.7438 (mt) cc_final: 0.7101 (mt) REVERT: F 245 MET cc_start: 0.3371 (ptt) cc_final: 0.3110 (ttp) REVERT: F 273 ILE cc_start: 0.7346 (tt) cc_final: 0.7101 (mt) REVERT: F 325 GLU cc_start: 0.7377 (tp30) cc_final: 0.6296 (tm-30) REVERT: F 423 LEU cc_start: 0.8270 (mt) cc_final: 0.7611 (tt) REVERT: F 590 ARG cc_start: 0.6593 (mmt-90) cc_final: 0.5555 (tpt170) REVERT: F 606 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7331 (pp) REVERT: F 629 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7753 (mtt180) REVERT: F 631 MET cc_start: 0.7601 (ttm) cc_final: 0.7316 (ttt) outliers start: 81 outliers final: 45 residues processed: 270 average time/residue: 0.4457 time to fit residues: 187.1983 Evaluate side-chains 228 residues out of total 3038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 178 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 742 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 633 ARG Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 829 HIS Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6937 > 50: distance: 74 - 79: 34.504 distance: 79 - 80: 31.143 distance: 80 - 81: 36.144 distance: 80 - 83: 44.084 distance: 81 - 82: 18.966 distance: 81 - 87: 20.748 distance: 83 - 84: 27.321 distance: 88 - 89: 31.102 distance: 88 - 91: 15.643 distance: 89 - 90: 18.497 distance: 89 - 95: 17.663 distance: 91 - 93: 8.953 distance: 92 - 94: 40.559 distance: 95 - 96: 41.997 distance: 96 - 97: 9.236 distance: 96 - 99: 29.471 distance: 97 - 106: 39.547 distance: 99 - 100: 22.163 distance: 100 - 101: 35.073 distance: 100 - 102: 15.304 distance: 101 - 103: 14.949 distance: 102 - 104: 14.978 distance: 103 - 105: 27.570 distance: 104 - 105: 15.669 distance: 106 - 107: 39.592 distance: 108 - 115: 7.762 distance: 110 - 111: 40.803 distance: 111 - 112: 11.248 distance: 112 - 113: 14.255 distance: 112 - 114: 44.242 distance: 115 - 116: 29.861 distance: 116 - 117: 20.263 distance: 117 - 119: 24.675 distance: 119 - 120: 25.382 distance: 120 - 121: 40.453 distance: 120 - 123: 40.176 distance: 121 - 122: 45.100 distance: 121 - 127: 49.754 distance: 123 - 124: 8.031 distance: 124 - 125: 39.854 distance: 124 - 126: 10.599 distance: 127 - 128: 29.125 distance: 128 - 129: 33.311 distance: 128 - 131: 41.955 distance: 129 - 130: 31.851 distance: 129 - 135: 42.868 distance: 130 - 160: 34.747 distance: 131 - 132: 29.787 distance: 132 - 133: 25.747 distance: 132 - 134: 28.296 distance: 135 - 136: 15.901 distance: 135 - 141: 6.659 distance: 136 - 137: 34.885 distance: 136 - 139: 10.846 distance: 137 - 138: 36.497 distance: 137 - 142: 41.548 distance: 140 - 141: 33.908 distance: 142 - 143: 37.165 distance: 143 - 144: 37.333 distance: 143 - 146: 25.895 distance: 144 - 145: 29.056 distance: 144 - 151: 38.951 distance: 146 - 147: 18.876 distance: 147 - 148: 13.447 distance: 148 - 149: 43.743 distance: 148 - 150: 34.571 distance: 151 - 152: 24.435 distance: 152 - 153: 19.282 distance: 152 - 155: 8.733 distance: 153 - 154: 30.222 distance: 153 - 160: 20.085 distance: 155 - 156: 10.198 distance: 156 - 157: 5.373 distance: 157 - 159: 5.524