Starting phenix.real_space_refine on Fri Dec 15 09:10:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6e_21553/12_2023/6w6e_21553_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6e_21553/12_2023/6w6e_21553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6e_21553/12_2023/6w6e_21553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6e_21553/12_2023/6w6e_21553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6e_21553/12_2023/6w6e_21553_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6e_21553/12_2023/6w6e_21553_neut_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 74 5.16 5 C 19113 2.51 5 N 5603 2.21 5 O 5981 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 279": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A ASP 566": "OD1" <-> "OD2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ASP 690": "OD1" <-> "OD2" Residue "A ASP 697": "OD1" <-> "OD2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A ASP 817": "OD1" <-> "OD2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ASP 356": "OD1" <-> "OD2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B ASP 435": "OD1" <-> "OD2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 622": "OD1" <-> "OD2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 626": "OD1" <-> "OD2" Residue "C TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 679": "OD1" <-> "OD2" Residue "C ASP 710": "OD1" <-> "OD2" Residue "C GLU 729": "OE1" <-> "OE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C ASP 766": "OD1" <-> "OD2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D GLU 628": "OE1" <-> "OE2" Residue "D ASP 635": "OD1" <-> "OD2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 679": "OD1" <-> "OD2" Residue "D GLU 680": "OE1" <-> "OE2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D ASP 766": "OD1" <-> "OD2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "D ASP 843": "OD1" <-> "OD2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E ASP 227": "OD1" <-> "OD2" Residue "E ASP 234": "OD1" <-> "OD2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ASP 264": "OD1" <-> "OD2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E ASP 346": "OD1" <-> "OD2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ASP 536": "OD1" <-> "OD2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ASP 566": "OD1" <-> "OD2" 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 635": "OD1" <-> "OD2" Residue "E TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 690": "OD1" <-> "OD2" Residue "E ASP 697": "OD1" <-> "OD2" Residue "E ASP 766": "OD1" <-> "OD2" Residue "E ARG 775": "NH1" <-> "NH2" Residue "E ASP 799": "OD1" <-> "OD2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "E ASP 817": "OD1" <-> "OD2" Residue "E ASP 832": "OD1" <-> "OD2" Residue "E ASP 843": "OD1" <-> "OD2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F ASP 278": "OD1" <-> "OD2" Residue "F TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F ARG 552": "NH1" <-> "NH2" Residue "F GLU 557": "OE1" <-> "OE2" 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 626": "OD1" <-> "OD2" Residue "F GLU 628": "OE1" <-> "OE2" Residue "F ASP 635": "OD1" <-> "OD2" Residue "F TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 641": "OE1" <-> "OE2" Residue "F ARG 669": "NH1" <-> "NH2" Residue "F GLU 680": "OE1" <-> "OE2" Residue "F ASP 687": "OD1" <-> "OD2" Residue "F ASP 690": "OD1" <-> "OD2" Residue "F PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 742": "OE1" <-> "OE2" Residue "F GLU 759": "OE1" <-> "OE2" Residue "F ASP 766": "OD1" <-> "OD2" Residue "F ARG 796": "NH1" <-> "NH2" Residue "F ASP 799": "OD1" <-> "OD2" Residue "F ASP 817": "OD1" <-> "OD2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30805 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5222 Classifications: {'peptide': 674} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4804 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 24, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4821 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 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: 4219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4219 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 24, 'TRANS': 521} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2694 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.19, per 1000 atoms: 0.56 Number of scatterers: 30805 At special positions: 0 Unit cell: (112.77, 142.842, 241.65, 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 74 16.00 P 34 15.00 O 5981 8.00 N 5603 7.00 C 19113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.71 Conformation dependent library (CDL) restraints added in 7.0 seconds 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7262 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 29 sheets defined 45.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 169 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 255 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: 3.952A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.530A pdb=" N ALA A 328 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA A 329 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 331 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 removed outlier: 5.352A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.912A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.791A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.541A pdb=" N ALA A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 493 removed outlier: 4.105A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 removed outlier: 4.000A pdb=" N GLU A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 537 through 547 removed outlier: 4.344A pdb=" N THR A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.880A pdb=" N LEU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.842A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 590 No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 615 through 623 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 647 removed outlier: 4.012A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (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 689 through 695 removed outlier: 5.048A pdb=" N GLN A 694 " --> pdb=" O ASP A 690 " (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 761 through 777 removed outlier: 3.780A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 805 through 823 removed outlier: 4.714A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.962A pdb=" N VAL B 284 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 317 through 323 removed outlier: 4.305A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 333 removed outlier: 4.037A pdb=" N ALA B 328 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA B 329 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 331 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG B 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 361 removed outlier: 3.935A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.796A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 407 removed outlier: 3.768A pdb=" N ILE B 392 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP B 393 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 removed outlier: 4.455A pdb=" N ILE B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 467 removed outlier: 3.826A pdb=" N ARG B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.977A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 590 removed outlier: 4.045A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.939A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 removed outlier: 3.647A pdb=" N VAL B 645 " --> pdb=" O LYS B 642 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 646 " --> pdb=" O HIS B 643 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 647 " --> pdb=" O THR B 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 642 through 647' Processing helix chain 'B' and resid 665 through 668 No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 688 through 694 removed outlier: 4.451A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 744 No H-bonds generated for 'chain 'B' and resid 741 through 744' Processing helix chain 'B' and resid 759 through 779 removed outlier: 4.687A pdb=" N ARG B 763 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 765 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 778 " --> pdb=" O ARG B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 795 removed outlier: 4.189A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 823 removed outlier: 3.765A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 4.228A 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 169 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 214 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 256 through 268 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.968A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 305' Processing helix chain 'C' and resid 325 through 333 removed outlier: 3.772A pdb=" N ALA C 328 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA C 329 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 331 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG C 332 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.704A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 368 through 380 removed outlier: 4.157A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.528A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.692A pdb=" N ALA C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 468 removed outlier: 4.216A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 558 through 570 removed outlier: 5.136A pdb=" N GLU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 590 removed outlier: 4.154A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 642 through 648 removed outlier: 3.568A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.536A pdb=" N LEU C 692 " --> pdb=" O PHE C 689 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 693 " --> pdb=" O ASP C 690 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN C 694 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 738 removed outlier: 4.458A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 744 No H-bonds generated for 'chain 'C' and resid 741 through 744' Processing helix chain 'C' and resid 761 through 779 removed outlier: 4.396A pdb=" N GLN C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 796 removed outlier: 3.787A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 825 removed outlier: 4.942A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.394A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 328 through 333 removed outlier: 4.989A pdb=" N ARG D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 361 removed outlier: 5.087A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 380 removed outlier: 4.244A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 406 removed outlier: 4.278A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 565 through 569 Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.771A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 643 through 648 removed outlier: 3.687A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'D' and resid 692 through 695 No H-bonds generated for 'chain 'D' and resid 692 through 695' Processing helix chain 'D' and resid 728 through 738 removed outlier: 4.230A pdb=" N ALA D 733 " --> pdb=" O GLU D 729 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA D 734 " --> pdb=" O GLN D 730 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG D 736 " --> pdb=" O LEU D 732 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 803 through 823 Proline residue: D 806 - end of helix removed outlier: 5.441A pdb=" N ARG D 809 " --> pdb=" O PRO D 806 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLY D 816 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP D 817 " --> pdb=" O ALA D 814 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS D 821 " --> pdb=" O GLN D 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.616A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 195 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 255 through 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 298 through 304 Proline residue: E 302 - end of helix No H-bonds generated for 'chain 'E' and resid 298 through 304' Processing helix chain 'E' and resid 317 through 323 Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 387 through 406 removed outlier: 4.108A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 546 removed outlier: 4.695A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 561 No H-bonds generated for 'chain 'E' and resid 558 through 561' Processing helix chain 'E' and resid 576 through 589 Processing helix chain 'E' and resid 613 through 625 removed outlier: 3.863A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 647 Processing helix chain 'E' and resid 688 through 697 Processing helix chain 'E' and resid 730 through 738 Processing helix chain 'E' and resid 743 through 746 removed outlier: 3.514A pdb=" N ARG E 746 " --> pdb=" O PHE E 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 743 through 746' Processing helix chain 'E' and resid 762 through 774 removed outlier: 4.196A pdb=" N LYS E 774 " --> pdb=" O ALA E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 797 removed outlier: 4.080A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 806 through 819 removed outlier: 4.096A pdb=" N VAL E 811 " --> pdb=" O LEU E 807 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 825 No H-bonds generated for 'chain 'E' and resid 822 through 825' Processing helix chain 'F' and resid 170 through 174 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 256 through 268 removed outlier: 3.910A pdb=" N LYS F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 344 through 358 removed outlier: 4.190A pdb=" N GLY F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP F 356 " --> pdb=" O ARG F 352 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG F 357 " --> pdb=" O GLY F 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR F 358 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 377 Processing helix chain 'F' and resid 387 through 405 removed outlier: 3.874A pdb=" N ILE F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 557 through 570 removed outlier: 5.488A pdb=" N GLU F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS F 570 " --> pdb=" O ASP F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 590 removed outlier: 4.005A pdb=" N VAL F 586 " --> pdb=" O VAL F 582 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 588 " --> pdb=" O ASP F 584 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 625 removed outlier: 3.566A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 647 removed outlier: 3.552A pdb=" N VAL F 645 " --> pdb=" O LYS F 642 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 669 Processing helix chain 'F' and resid 681 through 683 No H-bonds generated for 'chain 'F' and resid 681 through 683' Processing helix chain 'F' and resid 688 through 698 removed outlier: 5.179A pdb=" N ASP F 697 " --> pdb=" O LEU F 693 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU F 698 " --> pdb=" O GLN F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 738 Processing helix chain 'F' and resid 758 through 777 removed outlier: 4.324A pdb=" N VAL F 762 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG F 763 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 777 " --> pdb=" O LYS F 774 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 796 Processing helix chain 'F' and resid 805 through 823 removed outlier: 4.391A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 58 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 69 through 72 Processing helix chain 'I' and resid 88 through 107 removed outlier: 3.553A pdb=" N ILE I 95 " --> pdb=" O ILE I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 136 Processing helix chain 'I' and resid 147 through 154 Processing helix chain 'I' and resid 201 through 220 Processing helix chain 'I' and resid 224 through 226 No H-bonds generated for 'chain 'I' and resid 224 through 226' Processing helix chain 'I' and resid 228 through 246 Processing helix chain 'I' and resid 275 through 300 removed outlier: 5.099A pdb=" N ASP I 284 " --> pdb=" O ARG I 280 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG I 288 " --> pdb=" O ASP I 284 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR I 289 " --> pdb=" O LEU I 285 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG I 290 " --> pdb=" O LEU I 286 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS I 291 " --> pdb=" O ASP I 287 " (cutoff:3.500A) Proline residue: I 292 - end of helix Processing helix chain 'I' and resid 304 through 306 No H-bonds generated for 'chain 'I' and resid 304 through 306' Processing helix chain 'I' and resid 315 through 318 Processing helix chain 'I' and resid 320 through 329 Processing helix chain 'I' and resid 344 through 356 Processing sheet with id= A, first strand: chain 'A' and resid 335 through 338 removed outlier: 6.748A pdb=" N GLY A 313 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 314 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.720A pdb=" N LEU A 716 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 679 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 700 through 702 removed outlier: 3.683A pdb=" N LEU A 701 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.790A pdb=" N ARG B 310 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 277 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL B 312 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 335 through 338 removed outlier: 6.512A pdb=" N GLY B 313 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N GLY B 206 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR B 315 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 601 through 604 Processing sheet with id= G, first strand: chain 'B' and resid 633 through 635 removed outlier: 6.163A pdb=" N LEU B 677 " --> pdb=" O ILE B 634 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.583A pdb=" N LEU B 701 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 782 through 785 removed outlier: 4.266A pdb=" N VAL B 834 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.060A pdb=" N GLN C 335 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 205 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL C 337 " --> pdb=" O ILE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 276 through 278 removed outlier: 6.357A pdb=" N VAL C 312 " --> pdb=" O ILE C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 632 through 635 removed outlier: 3.507A pdb=" N ASP C 679 " --> pdb=" O ILE C 634 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 700 through 702 removed outlier: 3.763A pdb=" N LEU C 701 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 783 through 785 removed outlier: 7.108A pdb=" N VAL C 834 " --> pdb=" O GLN C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 165 through 167 removed outlier: 3.622A pdb=" N THR D 166 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 239 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 335 through 338 removed outlier: 6.816A pdb=" N GLY D 313 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 633 through 635 removed outlier: 6.240A pdb=" N LEU D 677 " --> pdb=" O ILE D 634 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 782 through 784 Processing sheet with id= S, first strand: chain 'E' and resid 335 through 339 removed outlier: 6.891A pdb=" N GLY E 313 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N GLY E 206 " --> pdb=" O GLY E 313 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N THR E 315 " --> pdb=" O GLY E 206 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 601 through 603 removed outlier: 3.778A pdb=" N PHE E 603 " --> pdb=" O LEU E 716 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 632 " --> pdb=" O LEU E 677 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP E 679 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE E 634 " --> pdb=" O ASP E 679 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 700 through 702 Processing sheet with id= V, first strand: chain 'F' and resid 276 through 278 removed outlier: 6.201A pdb=" N VAL F 312 " --> pdb=" O ILE F 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 751 through 753 removed outlier: 7.196A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE F 634 " --> pdb=" O ASP F 679 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 700 through 702 removed outlier: 3.638A pdb=" N LEU F 701 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 709 " --> pdb=" O LEU F 701 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'I' and resid 140 through 146 removed outlier: 7.729A pdb=" N ILE I 116 " --> pdb=" O LEU I 142 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE I 144 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR I 118 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN I 146 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL I 5 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR I 117 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE I 7 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL I 16 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= AA, first strand: chain 'I' and resid 78 through 81 Processing sheet with id= AB, first strand: chain 'I' and resid 309 through 313 removed outlier: 5.934A pdb=" N GLU I 182 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL I 190 " --> pdb=" O GLU I 182 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY I 184 " --> pdb=" O VAL I 188 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL I 188 " --> pdb=" O GLY I 184 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 250 through 255 1052 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.48 Time building geometry restraints manager: 13.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 10714 1.35 - 1.50: 7212 1.50 - 1.65: 13155 1.65 - 1.80: 90 1.80 - 1.95: 48 Bond restraints: 31219 Sorted by residual: bond pdb=" CA VAL I 115 " pdb=" C VAL I 115 " ideal model delta sigma weight residual 1.522 1.349 0.173 1.21e-02 6.83e+03 2.04e+02 bond pdb=" CA VAL A 473 " pdb=" C VAL A 473 " ideal model delta sigma weight residual 1.523 1.406 0.117 1.27e-02 6.20e+03 8.53e+01 bond pdb=" CA LEU I 167 " pdb=" C LEU I 167 " ideal model delta sigma weight residual 1.523 1.410 0.113 1.23e-02 6.61e+03 8.45e+01 bond pdb=" CA ILE I 95 " pdb=" C ILE I 95 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.23e-02 6.61e+03 8.35e+01 bond pdb=" N ASP I 8 " pdb=" CA ASP I 8 " ideal model delta sigma weight residual 1.463 1.348 0.114 1.28e-02 6.10e+03 7.98e+01 ... (remaining 31214 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.84: 895 106.84 - 114.09: 18279 114.09 - 121.33: 15279 121.33 - 128.58: 7627 128.58 - 135.82: 152 Bond angle restraints: 42232 Sorted by residual: angle pdb=" C MET I 319 " pdb=" N PRO I 320 " pdb=" CA PRO I 320 " ideal model delta sigma weight residual 119.56 128.64 -9.08 1.01e+00 9.80e-01 8.07e+01 angle pdb=" N ILE B 413 " pdb=" CA ILE B 413 " pdb=" C ILE B 413 " ideal model delta sigma weight residual 113.47 104.85 8.62 1.01e+00 9.80e-01 7.28e+01 angle pdb=" C ASN I 340 " pdb=" N PRO I 341 " pdb=" CA PRO I 341 " ideal model delta sigma weight residual 119.47 128.84 -9.37 1.16e+00 7.43e-01 6.52e+01 angle pdb=" C LEU I 255 " pdb=" N PRO I 256 " pdb=" CA PRO I 256 " ideal model delta sigma weight residual 119.85 127.13 -7.28 1.01e+00 9.80e-01 5.20e+01 angle pdb=" C GLU I 334 " pdb=" N PRO I 335 " pdb=" CA PRO I 335 " ideal model delta sigma weight residual 119.76 126.17 -6.41 1.00e+00 1.00e+00 4.11e+01 ... (remaining 42227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 18757 33.71 - 67.43: 487 67.43 - 101.14: 25 101.14 - 134.86: 0 134.86 - 168.57: 1 Dihedral angle restraints: 19270 sinusoidal: 8002 harmonic: 11268 Sorted by residual: dihedral pdb=" CA LEU B 387 " pdb=" C LEU B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -118.04 -61.96 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual 300.00 131.43 168.57 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA LYS I 333 " pdb=" C LYS I 333 " pdb=" N GLU I 334 " pdb=" CA GLU I 334 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 19267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3835 0.059 - 0.118: 852 0.118 - 0.176: 123 0.176 - 0.235: 23 0.235 - 0.294: 9 Chirality restraints: 4842 Sorted by residual: chirality pdb=" CA ALA I 349 " pdb=" N ALA I 349 " pdb=" C ALA I 349 " pdb=" CB ALA I 349 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ILE I 7 " pdb=" N ILE I 7 " pdb=" C ILE I 7 " pdb=" CB ILE I 7 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA VAL I 40 " pdb=" N VAL I 40 " pdb=" C VAL I 40 " pdb=" CB VAL I 40 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4839 not shown) Planarity restraints: 5533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 333 " 0.069 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C LYS I 333 " -0.249 2.00e-02 2.50e+03 pdb=" O LYS I 333 " 0.097 2.00e-02 2.50e+03 pdb=" N GLU I 334 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 491 " 0.025 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C GLU A 491 " -0.088 2.00e-02 2.50e+03 pdb=" O GLU A 491 " 0.033 2.00e-02 2.50e+03 pdb=" N ARG A 492 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 500 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ALA A 500 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA A 500 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU A 501 " 0.027 2.00e-02 2.50e+03 ... (remaining 5530 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 6 1.83 - 2.60: 399 2.60 - 3.37: 41071 3.37 - 4.13: 68522 4.13 - 4.90: 126039 Nonbonded interactions: 236037 Sorted by model distance: nonbonded pdb=" CZ ARG A 462 " pdb=" CE MET A 528 " model vdw 1.067 3.690 nonbonded pdb=" NH2 ARG A 462 " pdb=" CE MET A 528 " model vdw 1.111 3.540 nonbonded pdb=" NH1 ARG A 462 " pdb=" SD MET A 528 " model vdw 1.424 2.880 nonbonded pdb=" NH1 ARG A 462 " pdb=" CE MET A 528 " model vdw 1.447 3.540 nonbonded pdb=" O ARG A 462 " pdb=" OE1 GLU A 466 " model vdw 1.510 3.040 ... (remaining 236032 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 469 or resid 530 through 845 or resid 901)) selection = (chain 'B' and (resid 159 through 288 or resid 296 through 845 or resid 901)) selection = (chain 'C' and (resid 159 through 288 or resid 296 through 845 or resid 901)) } ncs_group { reference = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 845 or resid 901)) selection = (chain 'F' and (resid 159 through 407 or resid 530 through 845 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 17.640 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 82.830 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.170 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.008 0.173 31219 Z= 0.559 Angle : 0.860 10.708 42232 Z= 0.536 Chirality : 0.052 0.294 4842 Planarity : 0.006 0.144 5533 Dihedral : 14.902 168.569 12008 Min Nonbonded Distance : 1.067 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.64 % Favored : 89.15 % Rotamer: Outliers : 0.53 % Allowed : 5.99 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -4.00 (0.11), residues: 3890 helix: -1.98 (0.10), residues: 1885 sheet: -3.32 (0.21), residues: 395 loop : -3.21 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 545 HIS 0.010 0.001 HIS E 829 PHE 0.012 0.001 PHE A 753 TYR 0.011 0.001 TYR D 164 ARG 0.005 0.000 ARG D 809 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 397 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 413 average time/residue: 0.5726 time to fit residues: 339.4266 Evaluate side-chains 173 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 2.970 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 13 average time/residue: 0.2320 time to fit residues: 9.4313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 355 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 268 ASN A 323 HIS A 361 HIS A 705 HIS A 784 GLN B 221 GLN B 361 HIS B 663 GLN B 685 HIS B 705 HIS B 812 GLN C 221 GLN C 323 HIS C 361 HIS C 643 HIS C 685 HIS C 730 GLN ** C 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 GLN ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 HIS ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 768 GLN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 818 GLN E 829 HIS F 268 ASN F 685 HIS F 713 ASN F 829 HIS I 254 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 31219 Z= 0.490 Angle : 0.836 14.235 42232 Z= 0.414 Chirality : 0.049 0.224 4842 Planarity : 0.006 0.105 5533 Dihedral : 10.531 174.693 4576 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.05 % Favored : 88.82 % Rotamer: Outliers : 2.62 % Allowed : 13.97 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.13), residues: 3890 helix: -0.98 (0.12), residues: 1859 sheet: -2.94 (0.21), residues: 455 loop : -2.83 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 545 HIS 0.007 0.002 HIS E 685 PHE 0.038 0.003 PHE B 605 TYR 0.020 0.002 TYR A 504 ARG 0.006 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 163 time to evaluate : 3.436 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: 84 outliers final: 52 residues processed: 235 average time/residue: 0.4506 time to fit residues: 170.5259 Evaluate side-chains 187 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 135 time to evaluate : 3.647 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 18 residues processed: 52 average time/residue: 0.2926 time to fit residues: 33.6396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 4.9990 chunk 110 optimal weight: 0.0060 chunk 296 optimal weight: 0.0030 chunk 242 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 356 optimal weight: 8.9990 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 chunk 353 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 overall best weight: 0.5810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN B 362 HIS C 335 GLN C 575 GLN C 663 GLN C 757 ASN D 298 ASN D 336 GLN ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 HIS ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 31219 Z= 0.157 Angle : 0.610 10.657 42232 Z= 0.303 Chirality : 0.042 0.194 4842 Planarity : 0.004 0.090 5533 Dihedral : 9.891 159.282 4576 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.35 % Favored : 91.54 % Rotamer: Outliers : 2.00 % Allowed : 14.72 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -2.11 (0.13), residues: 3890 helix: -0.32 (0.12), residues: 1851 sheet: -2.52 (0.22), residues: 441 loop : -2.32 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 545 HIS 0.008 0.001 HIS E 281 PHE 0.017 0.001 PHE F 605 TYR 0.021 0.001 TYR D 251 ARG 0.005 0.000 ARG E 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 166 time to evaluate : 5.804 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: 64 outliers final: 36 residues processed: 223 average time/residue: 0.4474 time to fit residues: 162.3687 Evaluate side-chains 164 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 3.743 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 18 residues processed: 36 average time/residue: 0.2589 time to fit residues: 23.4680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 357 optimal weight: 2.9990 chunk 378 optimal weight: 30.0000 chunk 186 optimal weight: 6.9990 chunk 339 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS B 827 GLN C 575 GLN D 336 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31219 Z= 0.268 Angle : 0.641 10.866 42232 Z= 0.313 Chirality : 0.044 0.282 4842 Planarity : 0.005 0.089 5533 Dihedral : 9.681 134.205 4576 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.61 % Favored : 90.28 % Rotamer: Outliers : 2.21 % Allowed : 16.41 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.84 (0.14), residues: 3890 helix: -0.09 (0.13), residues: 1856 sheet: -2.49 (0.22), residues: 460 loop : -2.15 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 545 HIS 0.008 0.001 HIS E 281 PHE 0.018 0.002 PHE B 605 TYR 0.022 0.001 TYR D 251 ARG 0.010 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 137 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 40 residues processed: 198 average time/residue: 0.4361 time to fit residues: 145.6403 Evaluate side-chains 168 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 3.949 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 18 residues processed: 40 average time/residue: 0.2786 time to fit residues: 26.3636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 0.0670 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 0.0170 chunk 323 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 340 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS C 575 GLN D 336 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 31219 Z= 0.142 Angle : 0.578 10.373 42232 Z= 0.282 Chirality : 0.042 0.211 4842 Planarity : 0.004 0.084 5533 Dihedral : 9.293 116.238 4576 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.12 % Favored : 91.77 % Rotamer: Outliers : 1.56 % Allowed : 17.37 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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 (0.14), residues: 3890 helix: 0.17 (0.13), residues: 1846 sheet: -2.27 (0.22), residues: 454 loop : -1.91 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 792 HIS 0.011 0.001 HIS E 281 PHE 0.018 0.001 PHE D 623 TYR 0.027 0.001 TYR D 251 ARG 0.004 0.000 ARG E 736 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 28 residues processed: 193 average time/residue: 0.4271 time to fit residues: 135.7485 Evaluate side-chains 158 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 3.648 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 28 average time/residue: 0.2645 time to fit residues: 19.1390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 379 optimal weight: 7.9990 chunk 314 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 362 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN D 336 GLN ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 GLN E 837 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 31219 Z= 0.513 Angle : 0.809 13.379 42232 Z= 0.393 Chirality : 0.049 0.261 4842 Planarity : 0.006 0.098 5533 Dihedral : 9.672 91.523 4576 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.39 % Favored : 89.46 % Rotamer: Outliers : 2.59 % Allowed : 18.15 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.88 (0.13), residues: 3890 helix: -0.14 (0.12), residues: 1864 sheet: -2.46 (0.22), residues: 451 loop : -2.18 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 545 HIS 0.010 0.002 HIS F 281 PHE 0.024 0.003 PHE C 605 TYR 0.022 0.002 TYR D 251 ARG 0.006 0.001 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 137 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 53 residues processed: 210 average time/residue: 0.4273 time to fit residues: 149.5841 Evaluate side-chains 179 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 126 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 18 residues processed: 53 average time/residue: 0.2824 time to fit residues: 33.3630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 236 optimal weight: 0.2980 chunk 230 optimal weight: 0.8980 chunk 174 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS C 757 ASN D 336 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 31219 Z= 0.151 Angle : 0.603 11.900 42232 Z= 0.295 Chirality : 0.042 0.190 4842 Planarity : 0.004 0.081 5533 Dihedral : 9.217 83.054 4576 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.87 % Favored : 92.03 % Rotamer: Outliers : 1.37 % Allowed : 19.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.35 (0.14), residues: 3890 helix: 0.26 (0.13), residues: 1856 sheet: -2.18 (0.23), residues: 452 loop : -1.85 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 792 HIS 0.010 0.001 HIS E 281 PHE 0.029 0.001 PHE D 623 TYR 0.020 0.001 TYR D 251 ARG 0.006 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 182 average time/residue: 0.4379 time to fit residues: 131.8842 Evaluate side-chains 150 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 3.802 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 23 average time/residue: 0.3099 time to fit residues: 18.2443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 6.9990 chunk 150 optimal weight: 0.0000 chunk 225 optimal weight: 0.0870 chunk 113 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 240 optimal weight: 8.9990 chunk 257 optimal weight: 0.0670 chunk 186 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS C 694 GLN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 768 GLN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 31219 Z= 0.140 Angle : 0.588 13.810 42232 Z= 0.285 Chirality : 0.041 0.204 4842 Planarity : 0.004 0.080 5533 Dihedral : 8.815 83.502 4576 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.05 % Favored : 91.85 % Rotamer: Outliers : 1.00 % Allowed : 19.78 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.06 (0.14), residues: 3890 helix: 0.49 (0.13), residues: 1845 sheet: -1.98 (0.23), residues: 451 loop : -1.69 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 792 HIS 0.008 0.001 HIS E 281 PHE 0.025 0.001 PHE D 623 TYR 0.008 0.001 TYR D 338 ARG 0.011 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 173 average time/residue: 0.4335 time to fit residues: 124.6653 Evaluate side-chains 148 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 4.098 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 23 average time/residue: 0.2870 time to fit residues: 17.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 4.9990 chunk 361 optimal weight: 8.9990 chunk 330 optimal weight: 20.0000 chunk 352 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 318 optimal weight: 0.1980 chunk 332 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN B 362 HIS C 694 GLN C 757 ASN D 837 ASN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31219 Z= 0.237 Angle : 0.623 13.981 42232 Z= 0.300 Chirality : 0.043 0.291 4842 Planarity : 0.004 0.087 5533 Dihedral : 8.896 83.945 4576 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.53 % Favored : 91.36 % Rotamer: Outliers : 0.97 % Allowed : 20.27 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.02 (0.14), residues: 3890 helix: 0.57 (0.13), residues: 1842 sheet: -2.01 (0.23), residues: 453 loop : -1.72 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 545 HIS 0.006 0.001 HIS E 281 PHE 0.017 0.001 PHE D 623 TYR 0.011 0.001 TYR D 251 ARG 0.009 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 27 residues processed: 156 average time/residue: 0.4410 time to fit residues: 114.6557 Evaluate side-chains 152 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 3.684 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 18 residues processed: 27 average time/residue: 0.2746 time to fit residues: 19.4673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 4.9990 chunk 372 optimal weight: 40.0000 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 310 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31219 Z= 0.318 Angle : 0.671 13.785 42232 Z= 0.324 Chirality : 0.045 0.287 4842 Planarity : 0.005 0.091 5533 Dihedral : 9.038 83.221 4576 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.31 % Favored : 90.59 % Rotamer: Outliers : 0.81 % Allowed : 20.37 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.14 (0.14), residues: 3890 helix: 0.49 (0.13), residues: 1848 sheet: -2.15 (0.23), residues: 449 loop : -1.78 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 545 HIS 0.008 0.001 HIS F 281 PHE 0.024 0.002 PHE D 623 TYR 0.013 0.001 TYR D 338 ARG 0.009 0.000 ARG B 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.4469 time to fit residues: 108.7791 Evaluate side-chains 136 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 3.729 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 21 average time/residue: 0.2843 time to fit residues: 16.7527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 286 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 319 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.092363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061802 restraints weight = 103136.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063082 restraints weight = 58583.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063986 restraints weight = 39583.089| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 31219 Z= 0.381 Angle : 0.705 11.145 42232 Z= 0.342 Chirality : 0.046 0.283 4842 Planarity : 0.005 0.093 5533 Dihedral : 9.200 80.172 4576 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.59 % Favored : 90.28 % Rotamer: Outliers : 0.87 % Allowed : 20.46 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.31 (0.14), residues: 3890 helix: 0.31 (0.13), residues: 1870 sheet: -2.09 (0.24), residues: 435 loop : -1.91 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 545 HIS 0.008 0.001 HIS F 281 PHE 0.017 0.002 PHE C 386 TYR 0.016 0.002 TYR D 251 ARG 0.006 0.000 ARG B 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5158.76 seconds wall clock time: 115 minutes 25.98 seconds (6925.98 seconds total)