Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 16:59:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6h_21555/04_2023/6w6h_21555_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6h_21555/04_2023/6w6h_21555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6h_21555/04_2023/6w6h_21555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6h_21555/04_2023/6w6h_21555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6h_21555/04_2023/6w6h_21555_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6h_21555/04_2023/6w6h_21555_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 69 5.16 5 C 17630 2.51 5 N 5185 2.21 5 O 5509 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 207": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ASP 687": "OD1" <-> "OD2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B ASP 687": "OD1" <-> "OD2" Residue "B ASP 710": "OD1" <-> "OD2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B ASP 766": "OD1" <-> "OD2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 796": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C GLU 659": "OE1" <-> "OE2" Residue "C GLU 666": "OE1" <-> "OE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 687": "OD1" <-> "OD2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "C ARG 796": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ASP 227": "OD1" <-> "OD2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "D ASP 540": "OD1" <-> "OD2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D ASP 584": "OD1" <-> "OD2" Residue "D ASP 595": "OD1" <-> "OD2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 626": "OD1" <-> "OD2" Residue "D GLU 628": "OE1" <-> "OE2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D ASP 679": "OD1" <-> "OD2" Residue "D ASP 697": "OD1" <-> "OD2" Residue "D GLU 742": "OE1" <-> "OE2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E ARG 385": "NH1" <-> "NH2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ASP 536": "OD1" <-> "OD2" Residue "E GLU 555": "OE1" <-> "OE2" Residue "E ARG 588": "NH1" <-> "NH2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E GLU 638": "OE1" <-> "OE2" Residue "E TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 679": "OD1" <-> "OD2" Residue "E GLU 680": "OE1" <-> "OE2" Residue "E ASP 687": "OD1" <-> "OD2" Residue "E ASP 710": "OD1" <-> "OD2" Residue "E GLU 729": "OE1" <-> "OE2" Residue "E ASP 749": "OD1" <-> "OD2" Residue "E GLU 759": "OE1" <-> "OE2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "E ASP 832": "OD1" <-> "OD2" Residue "E ASP 841": "OD1" <-> "OD2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 230": "OE1" <-> "OE2" Residue "F ASP 241": "OD1" <-> "OD2" Residue "F ASP 327": "OD1" <-> "OD2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F ASP 356": "OD1" <-> "OD2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ASP 379": "OD1" <-> "OD2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ASP 407": "OD1" <-> "OD2" Residue "F ASP 414": "OD1" <-> "OD2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F ASP 435": "OD1" <-> "OD2" Residue "F GLU 448": "OE1" <-> "OE2" Residue "F GLU 531": "OE1" <-> "OE2" Residue "F ASP 536": "OD1" <-> "OD2" Residue "F ARG 552": "NH1" <-> "NH2" Residue "F ASP 566": "OD1" <-> "OD2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 622": "OD1" <-> "OD2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 641": "OE1" <-> "OE2" Residue "F ARG 669": "NH1" <-> "NH2" Residue "F PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F ASP 799": "OD1" <-> "OD2" Residue "F ASP 841": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28427 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: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4872 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4918 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 611} 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: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 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: 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: "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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" 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} Time building chain proxies: 13.60, per 1000 atoms: 0.48 Number of scatterers: 28427 At special positions: 0 Unit cell: (134.25, 154.656, 136.398, 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 69 16.00 P 34 15.00 O 5509 8.00 N 5185 7.00 C 17630 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.76 Conformation dependent library (CDL) restraints added in 4.2 seconds 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 19 sheets defined 45.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 168 through 173 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 254 through 268 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 301 through 304 No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.332A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.655A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 344 through 361 removed outlier: 3.815A pdb=" N GLY A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.638A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.515A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.652A pdb=" N ALA A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 468 removed outlier: 4.160A pdb=" N GLU A 440 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 441 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 443 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 444 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 445 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG A 446 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 454 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP A 463 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 3.691A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.740A pdb=" N LEU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.857A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 620 Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.539A pdb=" N VAL A 645 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 649 " --> pdb=" O ALA A 646 " (cutoff:3.500A) 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 692 through 698 removed outlier: 5.488A pdb=" N ASP A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) 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 759 through 779 removed outlier: 3.640A pdb=" N VAL A 762 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 763 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP A 766 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 777 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 778 " --> pdb=" O ARG A 775 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 779 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.950A pdb=" N ALA A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 814 removed outlier: 3.654A pdb=" N GLN A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.715A pdb=" N LEU A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 825 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 169 through 172 No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 184 through 193 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 320 through 323 No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 344 through 361 removed outlier: 5.297A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 377 Processing helix chain 'B' and resid 392 through 406 Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.576A pdb=" N ARG B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 476 removed outlier: 3.563A pdb=" N ALA B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 removed outlier: 3.560A pdb=" N ALA B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 576 through 590 removed outlier: 3.720A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 removed outlier: 3.674A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 622 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 649 removed outlier: 3.641A pdb=" N VAL B 645 " --> pdb=" O LYS B 642 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 646 " --> pdb=" O HIS B 643 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 649 " --> pdb=" O ALA B 646 " (cutoff:3.500A) 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 689 through 695 removed outlier: 4.629A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 695 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 738 removed outlier: 3.563A pdb=" N VAL B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 779 removed outlier: 3.506A pdb=" N ILE B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN B 778 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG B 779 " --> pdb=" O ARG B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 4.065A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 825 removed outlier: 3.514A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 5.010A 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 184 through 193 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 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 301 through 304 No H-bonds generated for 'chain 'C' and resid 301 through 304' Processing helix chain 'C' and resid 318 through 321 No H-bonds generated for 'chain 'C' and resid 318 through 321' Processing helix chain 'C' and resid 325 through 333 removed outlier: 3.660A pdb=" N ALA C 328 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA C 329 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG C 332 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.728A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 361 No H-bonds generated for 'chain 'C' and resid 358 through 361' Processing helix chain 'C' and resid 368 through 377 removed outlier: 3.608A pdb=" N THR C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 406 Processing helix chain 'C' and resid 414 through 427 Processing helix chain 'C' and resid 439 through 475 removed outlier: 3.926A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 Processing helix chain 'C' and resid 558 through 562 Processing helix chain 'C' and resid 564 through 567 No H-bonds generated for 'chain 'C' and resid 564 through 567' Processing helix chain 'C' and resid 576 through 590 removed outlier: 3.787A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 623 removed outlier: 3.592A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 622 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 647 removed outlier: 3.811A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 647 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 669 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 696 No H-bonds generated for 'chain 'C' and resid 693 through 696' Processing helix chain 'C' and resid 732 through 738 removed outlier: 3.847A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 746 removed outlier: 4.230A pdb=" N ARG C 746 " --> pdb=" O GLU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 776 removed outlier: 4.075A pdb=" N VAL C 762 " --> pdb=" O PRO C 758 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 removed outlier: 3.957A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 824 removed outlier: 3.901A pdb=" N GLN C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 212 through 225 removed outlier: 3.857A 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 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.884A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 4.244A pdb=" N VAL D 284 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.828A pdb=" N ALA D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 306' Processing helix chain 'D' and resid 317 through 323 removed outlier: 4.073A pdb=" N ARG D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 368 through 380 removed outlier: 3.960A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 557 through 570 removed outlier: 5.089A pdb=" N GLU D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 567 " --> pdb=" O ARG D 563 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 570 " --> pdb=" O ASP D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.806A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 Processing helix chain 'D' and resid 642 through 647 removed outlier: 3.568A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 642 through 647' Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 689 through 692 No H-bonds generated for 'chain 'D' and resid 689 through 692' 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 760 through 775 removed outlier: 3.537A pdb=" N ILE D 764 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 807 through 824 removed outlier: 4.395A pdb=" N ASP D 817 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.802A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 174' Processing helix chain 'E' and resid 185 through 194 Processing helix chain 'E' and resid 212 through 225 removed outlier: 3.687A pdb=" N ALA E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' 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 257 through 269 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 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 317 through 323 removed outlier: 3.602A pdb=" N LYS E 322 " --> pdb=" O ASP E 318 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 356 through 359 Processing helix chain 'E' and resid 368 through 380 removed outlier: 3.924A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 393 removed outlier: 4.740A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 393 " --> pdb=" O ASP E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 535 through 546 removed outlier: 4.712A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 569 No H-bonds generated for 'chain 'E' and resid 566 through 569' Processing helix chain 'E' and resid 576 through 590 removed outlier: 3.728A pdb=" N SER E 589 " --> pdb=" O ALA E 585 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG E 590 " --> pdb=" O VAL E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 613 through 624 Processing helix chain 'E' and resid 642 through 648 removed outlier: 5.534A pdb=" N ALA E 646 " --> pdb=" O HIS E 643 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 669 No H-bonds generated for 'chain 'E' and resid 666 through 669' 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 removed outlier: 3.649A pdb=" N GLN E 694 " --> pdb=" O ASP E 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 738 Processing helix chain 'E' and resid 741 through 746 Processing helix chain 'E' and resid 758 through 773 removed outlier: 3.973A pdb=" N VAL E 762 " --> pdb=" O PRO E 758 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG E 763 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 764 " --> pdb=" O GLU E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 795 Processing helix chain 'E' and resid 805 through 825 removed outlier: 3.861A pdb=" N ARG E 808 " --> pdb=" O ARG E 805 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL E 811 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA E 814 " --> pdb=" O VAL E 811 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 815 " --> pdb=" O GLN E 812 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY E 816 " --> pdb=" O GLN E 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP E 817 " --> pdb=" O ALA E 814 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 819 " --> pdb=" O GLY E 816 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 213 through 225 Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 280 through 284 removed outlier: 3.726A pdb=" N ILE F 283 " --> pdb=" O LEU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.824A pdb=" N ARG F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 326 removed outlier: 3.630A pdb=" N ARG F 321 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 322 " --> pdb=" O ASP F 318 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS F 326 " --> pdb=" O LYS F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.526A pdb=" N ARG F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 328 through 333' Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 368 through 377 removed outlier: 3.661A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 407 Processing helix chain 'F' and resid 414 through 430 removed outlier: 3.652A pdb=" N ILE F 425 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 426 " --> pdb=" O ARG F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 468 removed outlier: 4.136A pdb=" N SER F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 544 removed outlier: 3.652A pdb=" N ALA F 544 " --> pdb=" O ASP F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 562 removed outlier: 4.432A pdb=" N ALA F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS F 560 " --> pdb=" O GLY F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 568 No H-bonds generated for 'chain 'F' and resid 565 through 568' Processing helix chain 'F' and resid 576 through 590 removed outlier: 3.657A pdb=" N ALA F 581 " --> pdb=" O ALA F 577 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 590 " --> pdb=" O VAL F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 624 removed outlier: 3.841A pdb=" N ALA F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 649 removed outlier: 3.662A pdb=" N VAL F 645 " --> pdb=" O LYS F 642 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG F 647 " --> pdb=" O THR F 644 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 648 " --> pdb=" O VAL F 645 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE F 649 " --> pdb=" O ALA F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 658 through 660 No H-bonds generated for 'chain 'F' and resid 658 through 660' Processing helix chain 'F' and resid 664 through 669 removed outlier: 3.700A pdb=" N VAL F 668 " --> pdb=" O LEU F 664 " (cutoff:3.500A) 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 695 removed outlier: 4.608A pdb=" N GLN F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL F 695 " --> pdb=" O VAL F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 738 Processing helix chain 'F' and resid 741 through 744 No H-bonds generated for 'chain 'F' and resid 741 through 744' Processing helix chain 'F' and resid 758 through 777 removed outlier: 3.873A pdb=" N VAL F 762 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG F 763 " --> pdb=" O GLU F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 795 removed outlier: 4.038A pdb=" N ALA F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 805 through 825 removed outlier: 3.537A pdb=" N ARG F 809 " --> pdb=" O ARG F 805 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA F 825 " --> pdb=" O LYS F 821 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 165 through 167 removed outlier: 3.700A pdb=" N ALA A 239 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE A 274 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 240 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 276 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 312 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 313 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 206 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN A 335 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 205 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 337 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 602 through 606 removed outlier: 6.592A pdb=" N LEU A 716 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 605 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 718 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 632 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP A 679 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE A 634 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 783 through 785 removed outlier: 7.278A pdb=" N VAL A 834 " --> pdb=" O GLN A 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.565A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG B 310 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 277 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 312 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 206 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN B 335 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE B 205 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 5.922A 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 606 removed outlier: 3.556A pdb=" N PHE B 603 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 718 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 720 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 676 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR B 719 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE B 678 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASP B 679 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 782 through 785 Processing sheet with id= G, first strand: chain 'C' and resid 165 through 167 removed outlier: 3.573A pdb=" N ALA C 239 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 335 through 338 removed outlier: 6.758A pdb=" N GLY C 313 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY C 206 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 315 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 4.019A 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 606 removed outlier: 3.655A pdb=" N PHE C 603 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER C 720 " --> pdb=" O PHE C 605 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C 632 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP C 679 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE C 634 " --> pdb=" O ASP C 679 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 783 through 785 removed outlier: 7.416A pdb=" N VAL C 834 " --> pdb=" O GLN C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 335 through 338 removed outlier: 7.048A pdb=" N GLY D 313 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY D 206 " --> pdb=" O GLY D 313 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR D 315 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 314 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 750 through 753 removed outlier: 8.178A pdb=" N LEU D 751 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET D 604 " --> pdb=" O LEU D 751 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE D 753 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU D 606 " --> pdb=" O PHE D 753 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE D 605 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER D 720 " --> pdb=" O PHE D 605 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY D 607 " --> pdb=" O SER D 720 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL D 632 " --> pdb=" O LEU D 677 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 335 through 338 removed outlier: 6.069A pdb=" N LEU E 311 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU E 204 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY E 313 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR E 275 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA E 314 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 277 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP E 278 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 631 through 635 removed outlier: 6.995A pdb=" N VAL E 675 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE E 634 " --> pdb=" O VAL E 675 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU E 677 " --> pdb=" O ILE E 634 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE E 715 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N PHE E 678 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE E 717 " --> pdb=" O PHE E 678 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 700 through 702 Processing sheet with id= P, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.326A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL F 312 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 206 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN F 335 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE F 205 " --> pdb=" O GLN F 335 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL F 337 " --> pdb=" O ILE F 205 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 751 through 753 removed outlier: 3.819A pdb=" N PHE F 605 " --> pdb=" O LEU F 718 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER F 720 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY F 607 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE F 634 " --> pdb=" O ASP F 679 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 700 through 702 Processing sheet with id= S, first strand: chain 'F' and resid 782 through 785 882 hydrogen bonds defined for protein. 2382 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: 8.18 Time building geometry restraints manager: 12.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 11235 1.39 - 1.56: 17395 1.56 - 1.73: 51 1.73 - 1.90: 118 1.90 - 2.07: 10 Bond restraints: 28809 Sorted by residual: bond pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.28e+01 bond pdb=" C4 AGS F 902 " pdb=" C5 AGS F 902 " ideal model delta sigma weight residual 1.386 1.468 -0.082 1.00e-02 1.00e+04 6.74e+01 bond pdb=" C5 AGS F 901 " pdb=" C6 AGS F 901 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.26e+01 bond pdb=" C5 AGS F 902 " pdb=" C6 AGS F 902 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.96e+01 bond pdb=" PG AGS F 901 " pdb=" S1G AGS F 901 " ideal model delta sigma weight residual 1.949 2.074 -0.125 2.00e-02 2.50e+03 3.92e+01 ... (remaining 28804 not shown) Histogram of bond angle deviations from ideal: 99.99 - 107.24: 899 107.24 - 114.50: 17102 114.50 - 121.75: 14372 121.75 - 129.00: 6474 129.00 - 136.25: 112 Bond angle restraints: 38959 Sorted by residual: angle pdb=" C5 AGS F 901 " pdb=" C4 AGS F 901 " pdb=" N3 AGS F 901 " ideal model delta sigma weight residual 126.80 118.68 8.12 7.41e-01 1.82e+00 1.20e+02 angle pdb=" C5 AGS F 902 " pdb=" C4 AGS F 902 " pdb=" N3 AGS F 902 " ideal model delta sigma weight residual 126.80 118.76 8.04 7.41e-01 1.82e+00 1.18e+02 angle pdb=" C4 AGS F 902 " pdb=" C5 AGS F 902 " pdb=" N7 AGS F 902 " ideal model delta sigma weight residual 110.73 106.56 4.17 4.52e-01 4.89e+00 8.53e+01 angle pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " pdb=" N7 AGS F 901 " ideal model delta sigma weight residual 110.73 106.58 4.15 4.52e-01 4.89e+00 8.44e+01 angle pdb=" C5 AGS F 902 " pdb=" N7 AGS F 902 " pdb=" C8 AGS F 902 " ideal model delta sigma weight residual 103.67 107.43 -3.76 4.26e-01 5.51e+00 7.80e+01 ... (remaining 38954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.88: 16852 28.88 - 57.75: 767 57.75 - 86.63: 70 86.63 - 115.50: 3 115.50 - 144.38: 3 Dihedral angle restraints: 17695 sinusoidal: 7323 harmonic: 10372 Sorted by residual: dihedral pdb=" CA LEU C 387 " pdb=" C LEU C 387 " pdb=" N PRO C 388 " pdb=" CA PRO C 388 " ideal model delta harmonic sigma weight residual 180.00 145.23 34.77 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA LEU D 387 " pdb=" C LEU D 387 " pdb=" N PRO D 388 " pdb=" CA PRO D 388 " ideal model delta harmonic sigma weight residual 180.00 146.06 33.94 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" O2A ADP E 902 " pdb=" O3A ADP E 902 " pdb=" PA ADP E 902 " pdb=" PB ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 62.19 -122.19 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 17692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2978 0.039 - 0.077: 1058 0.077 - 0.116: 341 0.116 - 0.155: 63 0.155 - 0.193: 11 Chirality restraints: 4451 Sorted by residual: chirality pdb=" CA ILE C 413 " pdb=" N ILE C 413 " pdb=" C ILE C 413 " pdb=" CB ILE C 413 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CB VAL F 246 " pdb=" CA VAL F 246 " pdb=" CG1 VAL F 246 " pdb=" CG2 VAL F 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA LEU C 430 " pdb=" N LEU C 430 " pdb=" C LEU C 430 " pdb=" CB LEU C 430 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 4448 not shown) Planarity restraints: 5102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO B 388 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 387 " -0.056 5.00e-02 4.00e+02 8.42e-02 1.14e+01 pdb=" N PRO C 388 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 387 " -0.052 5.00e-02 4.00e+02 7.82e-02 9.79e+00 pdb=" N PRO D 388 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 388 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 388 " -0.043 5.00e-02 4.00e+02 ... (remaining 5099 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.75: 6 1.75 - 2.54: 228 2.54 - 3.32: 34586 3.32 - 4.11: 63312 4.11 - 4.90: 119684 Warning: very small nonbonded interaction distances. Nonbonded interactions: 217816 Sorted by model distance: nonbonded pdb=" O VAL C 411 " pdb=" OE1 GLU C 412 " model vdw 0.962 3.040 nonbonded pdb=" C VAL C 411 " pdb=" OE1 GLU C 412 " model vdw 0.983 3.270 nonbonded pdb=" OE2 GLU C 426 " pdb=" NH1 ARG D 352 " model vdw 1.139 2.520 nonbonded pdb=" O GLU C 424 " pdb=" SD MET C 428 " model vdw 1.154 3.400 nonbonded pdb=" O VAL C 411 " pdb=" CD GLU C 412 " model vdw 1.688 3.270 ... (remaining 217811 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 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'B' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'C' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'D' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'E' and resid 159 through 845) selection = (chain 'F' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) } 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: 3.510 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: 0.020 Extract box with map and model: 12.920 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 66.890 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.004 0.125 28809 Z= 0.262 Angle : 0.769 13.287 38959 Z= 0.494 Chirality : 0.044 0.193 4451 Planarity : 0.005 0.085 5102 Dihedral : 15.483 144.376 11009 Min Nonbonded Distance : 0.962 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.87 % Favored : 89.94 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.10 % 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: -4.10 (0.12), residues: 3577 helix: -2.08 (0.11), residues: 1718 sheet: -3.08 (0.22), residues: 371 loop : -3.32 (0.14), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 3.445 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: 41 outliers final: 26 residues processed: 315 average time/residue: 0.5220 time to fit residues: 240.5175 Evaluate side-chains 174 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 3.958 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 26 average time/residue: 0.3172 time to fit residues: 18.9874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 10.0000 chunk 273 optimal weight: 0.0020 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 210 optimal weight: 0.9980 chunk 327 optimal weight: 20.0000 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS A 812 GLN B 272 GLN B 361 HIS B 643 HIS ** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN C 685 HIS C 730 GLN C 827 GLN D 643 HIS D 757 ASN E 268 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 ASN F 281 HIS F 361 HIS F 643 HIS F 745 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28809 Z= 0.170 Angle : 0.619 13.110 38959 Z= 0.308 Chirality : 0.042 0.244 4451 Planarity : 0.005 0.084 5102 Dihedral : 8.144 132.742 4129 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.25 % Favored : 90.66 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.10 % 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: -2.94 (0.13), residues: 3577 helix: -1.09 (0.12), residues: 1752 sheet: -2.62 (0.23), residues: 368 loop : -2.77 (0.15), residues: 1457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 168 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 204 average time/residue: 0.3842 time to fit residues: 129.6925 Evaluate side-chains 174 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 10 residues processed: 25 average time/residue: 0.2477 time to fit residues: 16.3380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 328 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 325 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 812 GLN A 827 GLN C 221 GLN C 468 ASN C 643 HIS C 829 HIS ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 HIS F 159 GLN F 818 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.072 28809 Z= 0.527 Angle : 0.782 12.476 38959 Z= 0.385 Chirality : 0.049 0.202 4451 Planarity : 0.006 0.090 5102 Dihedral : 8.555 131.831 4129 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.29 % Favored : 88.59 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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: -2.69 (0.14), residues: 3577 helix: -0.88 (0.12), residues: 1755 sheet: -2.50 (0.24), residues: 378 loop : -2.65 (0.16), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 148 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 47 residues processed: 225 average time/residue: 0.3796 time to fit residues: 142.3760 Evaluate side-chains 179 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 132 time to evaluate : 3.301 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 19 residues processed: 47 average time/residue: 0.2479 time to fit residues: 26.5059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 329 optimal weight: 2.9990 chunk 348 optimal weight: 0.0070 chunk 172 optimal weight: 0.0050 chunk 312 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 28809 Z= 0.147 Angle : 0.606 15.023 38959 Z= 0.294 Chirality : 0.041 0.191 4451 Planarity : 0.005 0.080 5102 Dihedral : 8.168 131.537 4129 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.72 % Favored : 91.19 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -2.22 (0.14), residues: 3577 helix: -0.51 (0.13), residues: 1740 sheet: -2.21 (0.24), residues: 374 loop : -2.40 (0.16), residues: 1463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 31 residues processed: 202 average time/residue: 0.3802 time to fit residues: 129.4831 Evaluate side-chains 175 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 3.185 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 19 residues processed: 31 average time/residue: 0.2564 time to fit residues: 19.7172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 28809 Z= 0.434 Angle : 0.713 14.058 38959 Z= 0.348 Chirality : 0.046 0.184 4451 Planarity : 0.006 0.086 5102 Dihedral : 8.360 134.391 4129 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.79 % Favored : 89.12 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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: -2.22 (0.14), residues: 3577 helix: -0.50 (0.13), residues: 1763 sheet: -2.20 (0.24), residues: 381 loop : -2.45 (0.16), residues: 1433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 142 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 48 residues processed: 207 average time/residue: 0.3759 time to fit residues: 131.2488 Evaluate side-chains 181 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 133 time to evaluate : 3.493 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 19 residues processed: 48 average time/residue: 0.2670 time to fit residues: 29.2356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.6980 chunk 314 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 28809 Z= 0.150 Angle : 0.583 15.710 38959 Z= 0.285 Chirality : 0.041 0.176 4451 Planarity : 0.005 0.077 5102 Dihedral : 7.989 132.721 4129 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.81 % Favored : 91.14 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.89 (0.14), residues: 3577 helix: -0.25 (0.13), residues: 1759 sheet: -2.03 (0.25), residues: 378 loop : -2.25 (0.17), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 202 average time/residue: 0.3838 time to fit residues: 129.1072 Evaluate side-chains 175 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 3.232 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 20 residues processed: 29 average time/residue: 0.2512 time to fit residues: 18.9665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 199 optimal weight: 0.5980 chunk 255 optimal weight: 0.4980 chunk 197 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 347 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 212 optimal weight: 0.4980 chunk 160 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 757 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.104 28809 Z= 0.148 Angle : 0.569 15.872 38959 Z= 0.276 Chirality : 0.041 0.174 4451 Planarity : 0.005 0.079 5102 Dihedral : 7.751 130.578 4129 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.89 % Favored : 91.08 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.64 (0.15), residues: 3577 helix: -0.05 (0.13), residues: 1741 sheet: -1.83 (0.25), residues: 375 loop : -2.13 (0.17), residues: 1461 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 193 average time/residue: 0.3767 time to fit residues: 120.4137 Evaluate side-chains 170 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 3.152 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 25 average time/residue: 0.2441 time to fit residues: 15.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 207 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 172 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 273 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN D 757 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.089 28809 Z= 0.140 Angle : 0.569 15.805 38959 Z= 0.274 Chirality : 0.041 0.175 4451 Planarity : 0.005 0.080 5102 Dihedral : 7.620 129.097 4129 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.55 % Favored : 91.42 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.48 (0.15), residues: 3577 helix: 0.07 (0.13), residues: 1742 sheet: -1.69 (0.25), residues: 375 loop : -2.06 (0.17), residues: 1460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 187 average time/residue: 0.4257 time to fit residues: 130.0335 Evaluate side-chains 164 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 3.653 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 25 average time/residue: 0.2512 time to fit residues: 16.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 324 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 254 optimal weight: 0.0970 chunk 99 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 306 optimal weight: 0.9990 chunk 323 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 268 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 28809 Z= 0.272 Angle : 0.625 15.393 38959 Z= 0.304 Chirality : 0.043 0.304 4451 Planarity : 0.005 0.081 5102 Dihedral : 7.728 130.717 4129 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.48 % Favored : 90.47 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.10 % 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: -1.49 (0.15), residues: 3577 helix: 0.10 (0.13), residues: 1736 sheet: -1.76 (0.25), residues: 380 loop : -2.07 (0.17), residues: 1461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 31 residues processed: 168 average time/residue: 0.4004 time to fit residues: 112.3071 Evaluate side-chains 161 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 31 average time/residue: 0.2710 time to fit residues: 20.7121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 209 optimal weight: 0.0040 chunk 162 optimal weight: 0.9980 chunk 238 optimal weight: 0.0050 chunk 359 optimal weight: 20.0000 chunk 331 optimal weight: 0.2980 chunk 286 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 overall best weight: 0.6608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.084 28809 Z= 0.144 Angle : 0.573 16.134 38959 Z= 0.276 Chirality : 0.041 0.263 4451 Planarity : 0.005 0.076 5102 Dihedral : 7.514 128.143 4129 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.64 % Favored : 91.33 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.31 (0.15), residues: 3577 helix: 0.21 (0.13), residues: 1732 sheet: -1.60 (0.25), residues: 365 loop : -1.96 (0.17), residues: 1480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 25 residues processed: 167 average time/residue: 0.3822 time to fit residues: 107.8587 Evaluate side-chains 158 residues out of total 2950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 3.359 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 25 average time/residue: 0.2541 time to fit residues: 16.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.100630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074419 restraints weight = 63548.342| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.84 r_work: 0.2916 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 28809 Z= 0.187 Angle : 0.583 15.773 38959 Z= 0.281 Chirality : 0.041 0.274 4451 Planarity : 0.005 0.079 5102 Dihedral : 7.469 127.592 4129 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.14 % Favored : 90.83 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.23 (0.15), residues: 3577 helix: 0.29 (0.13), residues: 1720 sheet: -1.58 (0.25), residues: 375 loop : -1.91 (0.17), residues: 1482 =============================================================================== Job complete usr+sys time: 4682.13 seconds wall clock time: 86 minutes 9.24 seconds (5169.24 seconds total)