Starting phenix.real_space_refine on Sat Feb 17 15:38:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/02_2024/6ut4_20865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/02_2024/6ut4_20865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/02_2024/6ut4_20865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/02_2024/6ut4_20865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/02_2024/6ut4_20865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/02_2024/6ut4_20865_updated.pdb" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 24 5.16 5 C 12412 2.51 5 N 3224 2.21 5 O 3442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C ARG 435": "NH1" <-> "NH2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E ARG 261": "NH1" <-> "NH2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E ARG 435": "NH1" <-> "NH2" Residue "E GLU 437": "OE1" <-> "OE2" Residue "E ARG 448": "NH1" <-> "NH2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "F ARG 200": "NH1" <-> "NH2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F GLU 431": "OE1" <-> "OE2" Residue "F ARG 457": "NH1" <-> "NH2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F GLU 462": "OE1" <-> "OE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 511": "OE1" <-> "OE2" Residue "F GLU 520": "OE1" <-> "OE2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "F GLU 563": "OE1" <-> "OE2" Residue "F GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19126 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3164 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 370} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3152 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3144 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3109 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3164 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3183 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.15, per 1000 atoms: 0.53 Number of scatterers: 19126 At special positions: 0 Unit cell: (136.25, 123.75, 88.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 18 15.00 Mg 6 11.99 O 3442 8.00 N 3224 7.00 C 12412 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=0, symmetry=0 Time building additional restraints: 7.55 Conformation dependent library (CDL) restraints added in 3.5 seconds 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 111 helices and 18 sheets defined 42.3% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 200 through 203 No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.625A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 278 through 291 removed outlier: 3.609A pdb=" N GLY A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 319 through 335 removed outlier: 4.140A pdb=" N GLU A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 366 No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 441 through 450 removed outlier: 3.613A pdb=" N LYS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 removed outlier: 3.526A pdb=" N ARG A 459 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 460 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU A 462 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS A 463 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 466 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 468 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 490 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'B' and resid 197 through 207 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 319 through 338 removed outlier: 4.609A pdb=" N GLU B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 337 " --> pdb=" O TRP B 333 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 366 No H-bonds generated for 'chain 'B' and resid 363 through 366' Processing helix chain 'B' and resid 370 through 373 Processing helix chain 'B' and resid 421 through 424 No H-bonds generated for 'chain 'B' and resid 421 through 424' Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.773A pdb=" N LYS B 458 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN B 461 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU B 462 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE B 468 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 469 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 490 Processing helix chain 'B' and resid 510 through 520 Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 574 through 581 Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.744A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 319 through 335 removed outlier: 3.936A pdb=" N GLU C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 363 through 366 No H-bonds generated for 'chain 'C' and resid 363 through 366' Processing helix chain 'C' and resid 369 through 373 removed outlier: 3.969A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'C' and resid 436 through 439 Processing helix chain 'C' and resid 441 through 448 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 463 through 470 removed outlier: 3.511A pdb=" N SER C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 490 Processing helix chain 'C' and resid 510 through 520 Processing helix chain 'C' and resid 522 through 528 Processing helix chain 'C' and resid 533 through 539 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.788A pdb=" N ILE C 583 " --> pdb=" O ALA C 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 207 removed outlier: 3.677A pdb=" N ASN D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 278 through 293 removed outlier: 4.136A pdb=" N GLU D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 319 through 335 removed outlier: 3.852A pdb=" N GLU D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 344 No H-bonds generated for 'chain 'D' and resid 341 through 344' Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 363 through 366 No H-bonds generated for 'chain 'D' and resid 363 through 366' Processing helix chain 'D' and resid 370 through 373 No H-bonds generated for 'chain 'D' and resid 370 through 373' Processing helix chain 'D' and resid 376 through 378 No H-bonds generated for 'chain 'D' and resid 376 through 378' Processing helix chain 'D' and resid 436 through 439 Processing helix chain 'D' and resid 443 through 448 Processing helix chain 'D' and resid 455 through 470 removed outlier: 4.302A pdb=" N GLU D 462 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D 463 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 466 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE D 468 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER D 469 " --> pdb=" O GLU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 492 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 510 through 519 Processing helix chain 'D' and resid 522 through 528 Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.779A pdb=" N ILE D 583 " --> pdb=" O ALA D 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 208 Processing helix chain 'E' and resid 221 through 232 Processing helix chain 'E' and resid 278 through 290 removed outlier: 3.616A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 removed outlier: 3.652A pdb=" N ARG E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 338 removed outlier: 3.589A pdb=" N GLY E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY E 338 " --> pdb=" O GLU E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 363 through 366 No H-bonds generated for 'chain 'E' and resid 363 through 366' Processing helix chain 'E' and resid 369 through 373 removed outlier: 4.027A pdb=" N LEU E 373 " --> pdb=" O LEU E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 425 removed outlier: 3.662A pdb=" N ARG E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 421 through 425' Processing helix chain 'E' and resid 436 through 439 Processing helix chain 'E' and resid 441 through 451 removed outlier: 3.804A pdb=" N LYS E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 471 removed outlier: 5.087A pdb=" N ASN E 461 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU E 466 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE E 468 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER E 469 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 492 removed outlier: 4.415A pdb=" N ARG E 488 " --> pdb=" O LYS E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 503 No H-bonds generated for 'chain 'E' and resid 501 through 503' Processing helix chain 'E' and resid 510 through 519 Processing helix chain 'E' and resid 522 through 528 Processing helix chain 'E' and resid 533 through 539 removed outlier: 3.725A pdb=" N TRP E 538 " --> pdb=" O GLU E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 583 removed outlier: 3.518A pdb=" N ILE E 583 " --> pdb=" O ALA E 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 208 Processing helix chain 'F' and resid 221 through 232 Processing helix chain 'F' and resid 278 through 292 Processing helix chain 'F' and resid 301 through 312 removed outlier: 3.838A pdb=" N ARG F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 335 removed outlier: 3.827A pdb=" N GLU F 323 " --> pdb=" O PRO F 319 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 344 No H-bonds generated for 'chain 'F' and resid 341 through 344' Processing helix chain 'F' and resid 358 through 360 No H-bonds generated for 'chain 'F' and resid 358 through 360' Processing helix chain 'F' and resid 363 through 373 removed outlier: 6.889A pdb=" N GLU F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU F 370 " --> pdb=" O ILE F 366 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE F 371 " --> pdb=" O PHE F 367 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.652A pdb=" N ARG F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 439 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 456 through 470 removed outlier: 3.838A pdb=" N LYS F 470 " --> pdb=" O GLU F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 492 removed outlier: 3.937A pdb=" N VAL F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing helix chain 'F' and resid 501 through 503 No H-bonds generated for 'chain 'F' and resid 501 through 503' Processing helix chain 'F' and resid 510 through 520 Processing helix chain 'F' and resid 522 through 528 Processing helix chain 'F' and resid 533 through 539 Processing helix chain 'F' and resid 574 through 581 Processing sheet with id= A, first strand: chain 'A' and resid 428 through 431 removed outlier: 8.774A pdb=" N VAL A 211 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE A 405 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 213 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY A 407 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY A 215 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N MET A 409 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 351 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE A 406 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 353 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 408 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 355 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN A 410 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 258 through 264 Processing sheet with id= C, first strand: chain 'A' and resid 552 through 554 Processing sheet with id= D, first strand: chain 'B' and resid 428 through 431 removed outlier: 8.133A pdb=" N VAL B 211 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE B 405 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU B 213 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 407 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B 351 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 406 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 353 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR B 408 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 355 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 258 through 262 Processing sheet with id= F, first strand: chain 'B' and resid 552 through 554 Processing sheet with id= G, first strand: chain 'C' and resid 428 through 431 removed outlier: 8.810A pdb=" N VAL C 211 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 405 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 213 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 407 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY C 215 " --> pdb=" O GLY C 407 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 409 " --> pdb=" O GLY C 215 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE C 351 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE C 406 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 353 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR C 408 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 355 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ASN C 410 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 258 through 262 Processing sheet with id= I, first strand: chain 'C' and resid 552 through 554 Processing sheet with id= J, first strand: chain 'D' and resid 428 through 431 removed outlier: 8.801A pdb=" N VAL D 211 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE D 405 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU D 213 " --> pdb=" O ILE D 405 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY D 407 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N GLY D 215 " --> pdb=" O GLY D 407 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET D 409 " --> pdb=" O GLY D 215 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE D 351 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE D 406 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU D 353 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR D 408 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 355 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN D 410 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 258 through 262 Processing sheet with id= L, first strand: chain 'D' and resid 552 through 554 Processing sheet with id= M, first strand: chain 'E' and resid 428 through 431 removed outlier: 8.908A pdb=" N VAL E 211 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE E 405 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU E 213 " --> pdb=" O ILE E 405 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY E 407 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N GLY E 215 " --> pdb=" O GLY E 407 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET E 409 " --> pdb=" O GLY E 215 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE E 351 " --> pdb=" O TYR E 404 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE E 406 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 353 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR E 408 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE E 355 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN E 410 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 258 through 263 Processing sheet with id= O, first strand: chain 'E' and resid 552 through 554 Processing sheet with id= P, first strand: chain 'F' and resid 428 through 431 removed outlier: 8.892A pdb=" N VAL F 211 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE F 405 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU F 213 " --> pdb=" O ILE F 405 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY F 407 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N GLY F 215 " --> pdb=" O GLY F 407 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N MET F 409 " --> pdb=" O GLY F 215 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 351 " --> pdb=" O TYR F 404 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE F 406 " --> pdb=" O PHE F 351 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 353 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR F 408 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 355 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN F 410 " --> pdb=" O ILE F 355 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 258 through 265 removed outlier: 3.773A pdb=" N LYS F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 552 through 554 588 hydrogen bonds defined for protein. 1626 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: 5.35 Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5906 1.34 - 1.46: 3854 1.46 - 1.58: 9724 1.58 - 1.70: 34 1.70 - 1.82: 38 Bond restraints: 19556 Sorted by residual: bond pdb=" C THR C 348 " pdb=" N PRO C 349 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.52e+00 bond pdb=" C THR F 348 " pdb=" N PRO F 349 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C THR D 348 " pdb=" N PRO D 349 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.24e+00 bond pdb=" C THR E 348 " pdb=" N PRO E 349 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.07e+00 bond pdb=" C THR B 237 " pdb=" N PRO B 238 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.42e+00 ... (remaining 19551 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.01: 387 106.01 - 113.05: 10425 113.05 - 120.09: 7376 120.09 - 127.13: 8061 127.13 - 134.17: 225 Bond angle restraints: 26474 Sorted by residual: angle pdb=" C LEU D 540 " pdb=" N ASN D 541 " pdb=" CA ASN D 541 " ideal model delta sigma weight residual 122.46 128.54 -6.08 1.41e+00 5.03e-01 1.86e+01 angle pdb=" C LEU A 540 " pdb=" N ASN A 541 " pdb=" CA ASN A 541 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C LEU B 540 " pdb=" N ASN B 541 " pdb=" CA ASN B 541 " ideal model delta sigma weight residual 122.46 128.31 -5.85 1.41e+00 5.03e-01 1.72e+01 angle pdb=" C LEU C 540 " pdb=" N ASN C 541 " pdb=" CA ASN C 541 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C LEU E 540 " pdb=" N ASN E 541 " pdb=" CA ASN E 541 " ideal model delta sigma weight residual 122.46 128.13 -5.67 1.41e+00 5.03e-01 1.62e+01 ... (remaining 26469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10467 17.90 - 35.79: 1016 35.79 - 53.69: 161 53.69 - 71.59: 31 71.59 - 89.48: 16 Dihedral angle restraints: 11691 sinusoidal: 4938 harmonic: 6753 Sorted by residual: dihedral pdb=" CA PHE C 427 " pdb=" C PHE C 427 " pdb=" N ALA C 428 " pdb=" CA ALA C 428 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA PHE E 427 " pdb=" C PHE E 427 " pdb=" N ALA E 428 " pdb=" CA ALA E 428 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" N GLU A 268 " pdb=" C GLU A 268 " pdb=" CA GLU A 268 " pdb=" CB GLU A 268 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.85e+01 ... (remaining 11688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2609 0.081 - 0.162: 261 0.162 - 0.243: 18 0.243 - 0.324: 1 0.324 - 0.404: 2 Chirality restraints: 2891 Sorted by residual: chirality pdb=" CA GLU A 268 " pdb=" N GLU A 268 " pdb=" C GLU A 268 " pdb=" CB GLU A 268 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB ILE F 416 " pdb=" CA ILE F 416 " pdb=" CG1 ILE F 416 " pdb=" CG2 ILE F 416 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB ILE B 354 " pdb=" CA ILE B 354 " pdb=" CG1 ILE B 354 " pdb=" CG2 ILE B 354 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2888 not shown) Planarity restraints: 3311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 251 " 0.012 2.00e-02 2.50e+03 1.74e-02 6.08e+00 pdb=" CG TYR E 251 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 251 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 251 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR E 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR E 251 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 251 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 251 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 395 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO F 396 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 395 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO B 396 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 396 " -0.032 5.00e-02 4.00e+02 ... (remaining 3308 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 356 2.67 - 3.23: 16906 3.23 - 3.78: 31282 3.78 - 4.34: 44912 4.34 - 4.90: 71950 Nonbonded interactions: 165406 Sorted by model distance: nonbonded pdb="MG MG C 702 " pdb=" O HOH C 801 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR F 222 " pdb="MG MG F 702 " model vdw 2.112 2.170 nonbonded pdb="MG MG B 702 " pdb=" O HOH C 802 " model vdw 2.115 2.170 nonbonded pdb=" O2B GSP D 701 " pdb="MG MG D 702 " model vdw 2.122 2.170 nonbonded pdb=" O2G GSP F 701 " pdb="MG MG F 702 " model vdw 2.122 2.170 ... (remaining 165401 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 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 263 or (resid 270 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 through \ 295 or (resid 296 through 298 and (name N or name CA or name C or name O or nam \ e CB )) or resid 299 through 301 or (resid 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 314 or (resid 315 and (name N or na \ me CA or name C or name O or name CB )) or resid 316 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 394 or (resid 395 and (name N or name CA or name C or name O or nam \ e CB )) or resid 396 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 439 or (resid 440 through 441 and ( \ name N or name CA or name C or name O or name CB )) or resid 442 through 444 or \ (resid 445 through 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 or (resid 448 through 459 and (name N or name CA or name C or name \ O or name CB )) or resid 460 through 493 or (resid 494 and (name N or name CA or \ name C or name O or name CB )) or resid 495 through 544 or (resid 545 through 5 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 548 or (res \ id 549 and (name N or name CA or name C or name O or name CB )) or resid 550 thr \ ough 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) \ or resid 554 through 555 or (resid 556 and (name N or name CA or name C or name \ O or name CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or \ name C or name O or name CB )) or resid 562 through 571 or (resid 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 through 584 or resi \ d 701 through 702)) selection = (chain 'B' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 242 or (resid 243 and (name \ N or name CA or name C or name O or name CB )) or resid 244 through 263 or resi \ d 270 through 292 or (resid 293 and (name N or name CA or name C or name O or na \ me CB )) or resid 294 through 300 or (resid 301 through 302 and (name N or name \ CA or name C or name O or name CB )) or resid 303 through 368 or (resid 369 and \ (name N or name CA or name C or name O or name CB )) or resid 370 through 394 or \ (resid 395 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 6 through 404 or (resid 405 and (name N or name CA or name C or name O or name C \ B )) or resid 406 through 417 or (resid 418 and (name N or name CA or name C or \ name O or name CB )) or resid 419 through 439 or (resid 440 through 441 and (nam \ e N or name CA or name C or name O or name CB )) or resid 442 through 444 or (re \ sid 445 through 446 and (name N or name CA or name C or name O or name CB )) or \ resid 447 or (resid 448 through 459 and (name N or name CA or name C or name O o \ r name CB )) or resid 460 through 493 or (resid 494 and (name N or name CA or na \ me C or name O or name CB )) or resid 495 through 545 or (resid 546 through 547 \ and (name N or name CA or name C or name O or name CB )) or resid 548 or (resid \ 549 and (name N or name CA or name C or name O or name CB )) or resid 550 throug \ h 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) or \ resid 554 through 555 or (resid 556 and (name N or name CA or name C or name O o \ r name CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or na \ me C or name O or name CB )) or resid 562 through 571 or (resid 572 and (name N \ or name CA or name C or name O or name CB )) or resid 573 through 584 or resid 7 \ 01 through 702)) selection = (chain 'C' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 292 or (resid 293 and (name \ N or name CA or name C or name O or name CB )) or resid 294 through 295 or (res \ id 296 through 298 and (name N or name CA or name C or name O or name CB )) or r \ esid 299 through 300 or (resid 301 through 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 314 or (resid 315 and (name N or na \ me CA or name C or name O or name CB )) or resid 316 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 through 394 or (resid 395 and (name N or name CA or name C \ or name O or name CB )) or resid 396 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 417 or (resid 418 a \ nd (name N or name CA or name C or name O or name CB )) or resid 419 through 439 \ or (resid 440 through 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 444 or (resid 445 through 446 and (name N or name CA or \ name C or name O or name CB )) or resid 447 or (resid 448 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 493 or (res \ id 494 and (name N or name CA or name C or name O or name CB )) or resid 495 thr \ ough 544 or (resid 545 through 547 and (name N or name CA or name C or name O or \ name CB )) or resid 548 or (resid 549 and (name N or name CA or name C or name \ O or name CB )) or resid 550 through 555 or (resid 556 and (name N or name CA or \ name C or name O or name CB )) or resid 557 through 560 or (resid 561 and (name \ N or name CA or name C or name O or name CB )) or resid 562 through 571 or (res \ id 572 and (name N or name CA or name C or name O or name CB )) or resid 573 thr \ ough 584 or resid 701 through 702)) selection = (chain 'D' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 270 or (resid 271 and (name \ N or name CA or name C or name O or name CB )) or resid 272 through 292 or (res \ id 293 and (name N or name CA or name C or name O or name CB )) or resid 294 thr \ ough 295 or (resid 296 through 298 and (name N or name CA or name C or name O or \ name CB )) or resid 299 through 300 or (resid 301 through 302 and (name N or na \ me CA or name C or name O or name CB )) or resid 303 through 314 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 through 317 \ or (resid 318 and (name N or name CA or name C or name O or name CB )) or resid \ 319 or (resid 320 through 321 and (name N or name CA or name C or name O or nam \ e CB )) or resid 322 through 368 or (resid 369 and (name N or name CA or name C \ or name O or name CB )) or resid 370 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 417 or (resid 418 a \ nd (name N or name CA or name C or name O or name CB )) or resid 419 through 452 \ or (resid 453 through 459 and (name N or name CA or name C or name O or name CB \ )) or resid 460 through 555 or (resid 556 and (name N or name CA or name C or n \ ame O or name CB )) or resid 557 through 584 or resid 701 through 702)) selection = (chain 'E' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 263 or (resid 270 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 through \ 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or r \ esid 294 through 295 or (resid 296 through 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 300 or (resid 301 through 302 and ( \ name N or name CA or name C or name O or name CB )) or resid 303 through 314 or \ (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ through 317 or (resid 318 and (name N or name CA or name C or name O or name CB \ )) or resid 319 or (resid 320 through 321 and (name N or name CA or name C or n \ ame O or name CB )) or resid 322 through 368 or (resid 369 and (name N or name C \ A or name C or name O or name CB )) or resid 370 through 394 or (resid 395 and ( \ name N or name CA or name C or name O or name CB )) or resid 396 through 417 or \ (resid 418 and (name N or name CA or name C or name O or name CB )) or resid 419 \ through 439 or (resid 440 through 441 and (name N or name CA or name C or name \ O or name CB )) or resid 442 through 445 or (resid 446 and (name N or name CA or \ name C or name O or name CB )) or resid 447 or (resid 448 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 493 or (res \ id 494 and (name N or name CA or name C or name O or name CB )) or resid 495 thr \ ough 546 or (resid 547 and (name N or name CA or name C or name O or name CB )) \ or resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 550 through 552 or (resid 553 and (name N or name CA or name C or n \ ame O or name CB )) or resid 554 through 560 or (resid 561 and (name N or name C \ A or name C or name O or name CB )) or resid 562 through 584 or resid 701 throug \ h 702)) selection = (chain 'F' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 262 or (resid 263 and (name \ N or name CA or name C or name O or name CB )) or (resid 270 through 271 and (n \ ame N or name CA or name C or name O or name CB )) or resid 272 through 292 or ( \ resid 293 and (name N or name CA or name C or name O or name CB )) or resid 294 \ through 295 or (resid 296 through 298 and (name N or name CA or name C or name O \ or name CB )) or resid 299 through 300 or (resid 301 through 302 and (name N or \ name CA or name C or name O or name CB )) or resid 303 through 314 or (resid 31 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 316 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or re \ sid 319 or (resid 320 through 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 368 or (resid 369 and (name N or name CA or name \ C or name O or name CB )) or resid 370 through 394 or (resid 395 and (name N or \ name CA or name C or name O or name CB )) or resid 396 through 404 or (resid 40 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 406 through \ 417 or (resid 418 and (name N or name CA or name C or name O or name CB )) or re \ sid 419 through 439 or (resid 440 through 441 and (name N or name CA or name C o \ r name O or name CB )) or resid 442 through 444 or (resid 445 through 446 and (n \ ame N or name CA or name C or name O or name CB )) or resid 447 through 452 or ( \ resid 453 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 493 or (resid 494 and (name N or name CA or name C or name O \ or name CB )) or resid 495 through 544 or (resid 545 through 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 or (resid 549 and (name \ N or name CA or name C or name O or name CB )) or resid 550 through 552 or (resi \ d 553 and (name N or name CA or name C or name O or name CB )) or resid 554 thro \ ugh 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) o \ r resid 557 through 584 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.010 Extract box with map and model: 4.890 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 51.150 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.080 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19556 Z= 0.277 Angle : 0.751 11.562 26474 Z= 0.411 Chirality : 0.050 0.404 2891 Planarity : 0.006 0.059 3311 Dihedral : 14.347 89.483 7361 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.14), residues: 2295 helix: -3.30 (0.10), residues: 1025 sheet: -2.40 (0.26), residues: 284 loop : -1.24 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 242 HIS 0.009 0.001 HIS E 248 PHE 0.018 0.002 PHE B 247 TYR 0.041 0.002 TYR E 251 ARG 0.005 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 308 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.8319 (m-80) cc_final: 0.7991 (m-10) REVERT: B 409 MET cc_start: 0.8136 (ttt) cc_final: 0.7845 (tmm) REVERT: B 435 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7454 (mtt180) REVERT: B 515 HIS cc_start: 0.8465 (m170) cc_final: 0.8057 (m90) REVERT: B 542 GLU cc_start: 0.8256 (pt0) cc_final: 0.7943 (pt0) REVERT: C 261 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7377 (mmm160) REVERT: C 305 HIS cc_start: 0.7562 (t70) cc_final: 0.7342 (t-90) REVERT: C 415 SER cc_start: 0.9072 (p) cc_final: 0.8816 (p) REVERT: C 446 LYS cc_start: 0.8608 (tmmt) cc_final: 0.8235 (ttmt) REVERT: C 577 ILE cc_start: 0.9153 (mm) cc_final: 0.8898 (mm) REVERT: D 253 TYR cc_start: 0.8738 (t80) cc_final: 0.8401 (t80) REVERT: D 255 GLU cc_start: 0.8060 (mp0) cc_final: 0.7328 (mp0) REVERT: F 518 TYR cc_start: 0.8538 (m-80) cc_final: 0.8297 (m-80) outliers start: 3 outliers final: 2 residues processed: 310 average time/residue: 0.3939 time to fit residues: 172.5456 Evaluate side-chains 196 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 3.9990 chunk 173 optimal weight: 0.0020 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 346 ASN A 461 ASN A 506 ASN A 515 HIS A 541 ASN B 248 HIS B 384 ASN B 443 ASN B 465 ASN B 473 ASN B 501 HIS B 561 ASN C 248 HIS C 249 GLN C 384 ASN C 497 HIS C 501 HIS C 541 ASN D 248 HIS ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 384 ASN E 384 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS F 384 ASN F 385 GLN F 461 ASN F 541 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19556 Z= 0.144 Angle : 0.488 8.278 26474 Z= 0.244 Chirality : 0.040 0.142 2891 Planarity : 0.004 0.049 3311 Dihedral : 5.739 47.174 2647 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.32 % Allowed : 9.97 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.25 (0.16), residues: 2295 helix: -1.73 (0.14), residues: 1040 sheet: -2.15 (0.26), residues: 294 loop : -0.70 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 333 HIS 0.004 0.001 HIS E 515 PHE 0.016 0.001 PHE A 477 TYR 0.015 0.001 TYR E 251 ARG 0.003 0.000 ARG C 435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 2.442 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7943 (tttm) cc_final: 0.7526 (tttm) REVERT: B 348 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6948 (m) REVERT: B 409 MET cc_start: 0.8077 (ttt) cc_final: 0.7717 (tmm) REVERT: B 435 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7360 (mtt180) REVERT: B 515 HIS cc_start: 0.8344 (m170) cc_final: 0.7988 (m90) REVERT: B 542 GLU cc_start: 0.8315 (pt0) cc_final: 0.7996 (pt0) REVERT: C 261 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7364 (mmm160) REVERT: D 253 TYR cc_start: 0.8709 (t80) cc_final: 0.8415 (t80) REVERT: D 255 GLU cc_start: 0.7921 (mp0) cc_final: 0.7137 (mp0) REVERT: D 470 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8019 (mttt) REVERT: E 466 GLU cc_start: 0.7490 (tp30) cc_final: 0.7263 (tp30) outliers start: 26 outliers final: 13 residues processed: 232 average time/residue: 0.3476 time to fit residues: 119.8452 Evaluate side-chains 206 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 225 optimal weight: 0.0980 chunk 185 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS F 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19556 Z= 0.175 Angle : 0.485 8.542 26474 Z= 0.241 Chirality : 0.040 0.146 2891 Planarity : 0.003 0.040 3311 Dihedral : 5.385 49.817 2646 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.32 % Allowed : 11.99 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.46 (0.17), residues: 2295 helix: -0.97 (0.15), residues: 1044 sheet: -1.97 (0.26), residues: 309 loop : -0.31 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.020 0.001 HIS D 305 PHE 0.014 0.001 PHE D 279 TYR 0.019 0.001 TYR E 322 ARG 0.007 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 2.265 Fit side-chains REVERT: A 333 TRP cc_start: 0.8480 (m100) cc_final: 0.8279 (m100) REVERT: A 519 TYR cc_start: 0.8193 (m-80) cc_final: 0.7818 (m-10) REVERT: B 348 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6941 (m) REVERT: B 357 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 435 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7376 (mtt180) REVERT: B 515 HIS cc_start: 0.8324 (m170) cc_final: 0.8004 (m90) REVERT: B 542 GLU cc_start: 0.8429 (pt0) cc_final: 0.8131 (pt0) REVERT: C 261 ARG cc_start: 0.7616 (mtt180) cc_final: 0.7266 (mmm160) REVERT: D 255 GLU cc_start: 0.7867 (mp0) cc_final: 0.7136 (mp0) REVERT: E 210 GLN cc_start: 0.8072 (mp10) cc_final: 0.7852 (mp10) REVERT: F 445 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8015 (ttmt) outliers start: 26 outliers final: 15 residues processed: 228 average time/residue: 0.3588 time to fit residues: 120.9441 Evaluate side-chains 214 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 139 optimal weight: 0.0970 chunk 209 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 109 optimal weight: 0.3980 chunk 198 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19556 Z= 0.174 Angle : 0.482 7.657 26474 Z= 0.239 Chirality : 0.040 0.144 2891 Planarity : 0.003 0.037 3311 Dihedral : 5.224 52.930 2646 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.77 % Allowed : 12.65 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.00 (0.17), residues: 2295 helix: -0.53 (0.16), residues: 1040 sheet: -1.82 (0.27), residues: 302 loop : -0.13 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.004 0.001 HIS A 515 PHE 0.013 0.001 PHE D 279 TYR 0.015 0.001 TYR E 325 ARG 0.004 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 2.405 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7817 (tttm) cc_final: 0.7596 (tttm) REVERT: A 574 ASP cc_start: 0.6940 (t0) cc_final: 0.6704 (t0) REVERT: B 249 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8035 (mm110) REVERT: B 348 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6927 (m) REVERT: B 357 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 435 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7421 (mtt180) REVERT: B 515 HIS cc_start: 0.8335 (m170) cc_final: 0.8022 (m90) REVERT: D 255 GLU cc_start: 0.7870 (mp0) cc_final: 0.7160 (mp0) REVERT: E 210 GLN cc_start: 0.8086 (mp10) cc_final: 0.7867 (mp10) REVERT: E 323 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6825 (pm20) REVERT: F 445 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8107 (ttmt) outliers start: 35 outliers final: 23 residues processed: 225 average time/residue: 0.3405 time to fit residues: 115.2981 Evaluate side-chains 218 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 521 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 4.9990 chunk 125 optimal weight: 0.0060 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 198 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19556 Z= 0.178 Angle : 0.478 6.873 26474 Z= 0.237 Chirality : 0.040 0.147 2891 Planarity : 0.003 0.037 3311 Dihedral : 5.122 56.775 2646 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.82 % Allowed : 13.26 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2295 helix: -0.22 (0.16), residues: 1036 sheet: -1.69 (0.27), residues: 312 loop : 0.05 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 242 HIS 0.004 0.001 HIS D 305 PHE 0.013 0.001 PHE D 279 TYR 0.016 0.001 TYR E 322 ARG 0.005 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 2.438 Fit side-chains revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8062 (tt0) cc_final: 0.7861 (tt0) REVERT: A 574 ASP cc_start: 0.7101 (t0) cc_final: 0.6896 (t0) REVERT: B 348 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6920 (m) REVERT: B 357 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 435 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7525 (mtt180) REVERT: B 515 HIS cc_start: 0.8351 (m170) cc_final: 0.8025 (m90) REVERT: C 261 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7190 (mmm160) REVERT: D 255 GLU cc_start: 0.7901 (mp0) cc_final: 0.7186 (mp0) REVERT: E 210 GLN cc_start: 0.8027 (mp10) cc_final: 0.7805 (mp10) REVERT: E 323 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: F 323 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7262 (mm-30) REVERT: F 445 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8128 (ttmt) outliers start: 36 outliers final: 27 residues processed: 226 average time/residue: 0.3436 time to fit residues: 116.1738 Evaluate side-chains 218 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 521 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 221 optimal weight: 0.4980 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 HIS ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19556 Z= 0.145 Angle : 0.465 6.466 26474 Z= 0.229 Chirality : 0.039 0.144 2891 Planarity : 0.003 0.036 3311 Dihedral : 4.933 57.253 2646 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.77 % Allowed : 13.77 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2295 helix: 0.03 (0.16), residues: 1036 sheet: -1.51 (0.28), residues: 317 loop : 0.12 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 242 HIS 0.005 0.001 HIS D 305 PHE 0.012 0.001 PHE D 279 TYR 0.016 0.001 TYR E 322 ARG 0.005 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 2.650 Fit side-chains revert: symmetry clash REVERT: A 292 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.6166 (m-80) REVERT: A 574 ASP cc_start: 0.7112 (t0) cc_final: 0.6903 (t0) REVERT: B 249 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8032 (mm110) REVERT: B 348 THR cc_start: 0.7127 (OUTLIER) cc_final: 0.6880 (m) REVERT: B 357 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 435 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7435 (mtt180) REVERT: B 515 HIS cc_start: 0.8299 (m170) cc_final: 0.7969 (m90) REVERT: D 255 GLU cc_start: 0.7883 (mp0) cc_final: 0.7179 (mp0) REVERT: E 294 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8721 (mp) REVERT: F 323 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7252 (mm-30) REVERT: F 445 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8035 (tttt) outliers start: 35 outliers final: 30 residues processed: 221 average time/residue: 0.3332 time to fit residues: 112.3969 Evaluate side-chains 224 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 521 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19556 Z= 0.254 Angle : 0.517 6.786 26474 Z= 0.257 Chirality : 0.041 0.151 2891 Planarity : 0.003 0.036 3311 Dihedral : 5.212 59.886 2646 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.18 % Allowed : 14.07 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2295 helix: -0.04 (0.16), residues: 1049 sheet: -1.50 (0.28), residues: 312 loop : 0.20 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 242 HIS 0.007 0.001 HIS D 305 PHE 0.013 0.001 PHE D 279 TYR 0.017 0.001 TYR E 322 ARG 0.006 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 2.367 Fit side-chains REVERT: A 292 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: A 574 ASP cc_start: 0.7130 (t0) cc_final: 0.6915 (t0) REVERT: B 348 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6875 (m) REVERT: B 357 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7681 (mm-30) REVERT: B 435 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7463 (mtt180) REVERT: B 515 HIS cc_start: 0.8426 (m170) cc_final: 0.8086 (m90) REVERT: B 542 GLU cc_start: 0.8488 (pt0) cc_final: 0.8189 (pt0) REVERT: C 261 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7214 (mmm160) REVERT: C 549 ASN cc_start: 0.8263 (m-40) cc_final: 0.7966 (p0) REVERT: D 255 GLU cc_start: 0.7909 (mp0) cc_final: 0.7195 (mp0) REVERT: E 294 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8818 (mp) REVERT: E 323 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6750 (pm20) REVERT: F 292 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: F 445 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8377 (ttmt) outliers start: 43 outliers final: 30 residues processed: 217 average time/residue: 0.3486 time to fit residues: 112.9342 Evaluate side-chains 218 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 0.0060 chunk 150 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19556 Z= 0.230 Angle : 0.506 8.410 26474 Z= 0.251 Chirality : 0.041 0.147 2891 Planarity : 0.003 0.036 3311 Dihedral : 5.173 59.112 2646 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.92 % Allowed : 14.57 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2295 helix: 0.04 (0.16), residues: 1052 sheet: -1.44 (0.29), residues: 312 loop : 0.29 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 242 HIS 0.005 0.001 HIS D 305 PHE 0.013 0.001 PHE D 279 TYR 0.018 0.001 TYR E 322 ARG 0.005 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: A 292 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: A 574 ASP cc_start: 0.7139 (t0) cc_final: 0.6928 (t0) REVERT: B 348 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6858 (m) REVERT: B 357 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 435 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7531 (mtt180) REVERT: B 515 HIS cc_start: 0.8430 (m170) cc_final: 0.8094 (m90) REVERT: B 542 GLU cc_start: 0.8456 (pt0) cc_final: 0.8143 (pt0) REVERT: C 261 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7214 (mmm160) REVERT: C 549 ASN cc_start: 0.8259 (m-40) cc_final: 0.7984 (p0) REVERT: E 294 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8823 (mp) REVERT: E 323 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: F 292 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6766 (m-10) REVERT: F 457 ARG cc_start: 0.8258 (mtm180) cc_final: 0.8022 (mmm-85) REVERT: F 520 GLU cc_start: 0.7455 (tt0) cc_final: 0.7218 (tp30) outliers start: 38 outliers final: 28 residues processed: 211 average time/residue: 0.3477 time to fit residues: 110.0659 Evaluate side-chains 213 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 185 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19556 Z= 0.229 Angle : 0.509 9.112 26474 Z= 0.252 Chirality : 0.041 0.147 2891 Planarity : 0.003 0.035 3311 Dihedral : 5.165 58.835 2646 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.87 % Allowed : 14.68 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2295 helix: 0.09 (0.16), residues: 1047 sheet: -1.37 (0.30), residues: 302 loop : 0.27 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 333 HIS 0.005 0.001 HIS D 305 PHE 0.014 0.001 PHE D 279 TYR 0.018 0.001 TYR E 322 ARG 0.005 0.000 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: A 292 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: A 574 ASP cc_start: 0.7155 (t0) cc_final: 0.6944 (t0) REVERT: B 348 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6850 (m) REVERT: B 357 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 435 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7532 (mtt180) REVERT: B 515 HIS cc_start: 0.8436 (m170) cc_final: 0.8071 (m90) REVERT: C 261 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7222 (mmm160) REVERT: C 532 ASP cc_start: 0.8405 (t0) cc_final: 0.8152 (t70) REVERT: E 294 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8811 (mp) REVERT: E 323 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: F 292 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6689 (m-10) REVERT: F 457 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7954 (mmm-85) REVERT: F 503 TYR cc_start: 0.8305 (m-80) cc_final: 0.7514 (m-80) outliers start: 37 outliers final: 29 residues processed: 209 average time/residue: 0.3531 time to fit residues: 110.9023 Evaluate side-chains 216 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 7.9990 chunk 217 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19556 Z= 0.217 Angle : 0.507 9.399 26474 Z= 0.252 Chirality : 0.041 0.148 2891 Planarity : 0.003 0.035 3311 Dihedral : 5.119 58.537 2646 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.92 % Allowed : 14.73 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2295 helix: 0.19 (0.16), residues: 1040 sheet: -1.29 (0.29), residues: 322 loop : 0.31 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 333 HIS 0.005 0.001 HIS D 305 PHE 0.013 0.001 PHE D 279 TYR 0.018 0.001 TYR E 322 ARG 0.005 0.000 ARG B 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 2.271 Fit side-chains REVERT: A 292 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: A 574 ASP cc_start: 0.7161 (t0) cc_final: 0.6957 (t0) REVERT: B 249 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8260 (mm110) REVERT: B 348 THR cc_start: 0.7090 (OUTLIER) cc_final: 0.6834 (m) REVERT: B 357 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 435 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7533 (mtt180) REVERT: B 515 HIS cc_start: 0.8432 (m170) cc_final: 0.8101 (m90) REVERT: C 261 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7219 (mmm160) REVERT: C 532 ASP cc_start: 0.8312 (t0) cc_final: 0.8065 (t70) REVERT: D 255 GLU cc_start: 0.7905 (mp0) cc_final: 0.7156 (mp0) REVERT: E 294 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8685 (mp) REVERT: E 323 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: F 292 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: F 457 ARG cc_start: 0.8212 (mtm180) cc_final: 0.7939 (mmm-85) REVERT: F 503 TYR cc_start: 0.8268 (m-80) cc_final: 0.7502 (m-80) outliers start: 38 outliers final: 31 residues processed: 205 average time/residue: 0.3518 time to fit residues: 108.1105 Evaluate side-chains 217 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 292 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 496 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 0.0060 chunk 181 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 186 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 ASN ** 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 = 0.3481 r_free = 0.3481 target = 0.126776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102673 restraints weight = 26489.119| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.79 r_work: 0.3002 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19556 Z= 0.138 Angle : 0.472 9.132 26474 Z= 0.233 Chirality : 0.040 0.150 2891 Planarity : 0.003 0.033 3311 Dihedral : 4.765 56.552 2646 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.77 % Allowed : 15.03 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2295 helix: 0.36 (0.16), residues: 1043 sheet: -1.26 (0.29), residues: 326 loop : 0.34 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 333 HIS 0.003 0.001 HIS D 514 PHE 0.012 0.001 PHE D 279 TYR 0.017 0.001 TYR E 322 ARG 0.005 0.000 ARG B 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.10 seconds wall clock time: 73 minutes 23.62 seconds (4403.62 seconds total)