Starting phenix.real_space_refine on Thu Feb 22 16:57:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y0c_10667/02_2024/6y0c_10667.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y0c_10667/02_2024/6y0c_10667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y0c_10667/02_2024/6y0c_10667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y0c_10667/02_2024/6y0c_10667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y0c_10667/02_2024/6y0c_10667.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y0c_10667/02_2024/6y0c_10667.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 S 132 5.16 5 C 11063 2.51 5 N 3001 2.21 5 O 3322 1.98 5 H 17430 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ARG 299": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A ARG 468": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A ARG 552": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 568": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 383": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "B ASP 566": "OD1" <-> "OD2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B ASP 618": "OD1" <-> "OD2" Residue "B ARG 624": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B ARG 663": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 690": "OD1" <-> "OD2" Residue "B PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 733": "OD1" <-> "OD2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B GLU 752": "OE1" <-> "OE2" Residue "C ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C ASP 260": "OD1" <-> "OD2" Residue "C ASP 265": "OD1" <-> "OD2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C ASP 315": "OD1" <-> "OD2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C ASP 421": "OD1" <-> "OD2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ASP 559": "OD1" <-> "OD2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C ARG 611": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ARG 656": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 692": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 703": "OD1" <-> "OD2" Residue "C PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34967 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 11153 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 31, 'TRANS': 656} Chain breaks: 2 Chain: "B" Number of atoms: 10982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 10982 Classifications: {'peptide': 686} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 660} Chain breaks: 5 Chain: "C" Number of atoms: 12190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 12190 Classifications: {'peptide': 761} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 732} Chain breaks: 1 Chain: "IN" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 642 Inner-chain residues flagged as termini: ['pdbres=" GIN 14 "'] Classifications: {'RNA': 20} Modifications used: {'3*END': 2, '5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 14} Chain breaks: 2 Time building chain proxies: 15.52, per 1000 atoms: 0.44 Number of scatterers: 34967 At special positions: 0 Unit cell: (124.775, 133.455, 109.585, 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 132 16.00 P 19 15.00 O 3322 8.00 N 3001 7.00 C 11063 6.00 H 17430 1.00 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: 29.07 Conformation dependent library (CDL) restraints added in 3.6 seconds 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4038 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 22 sheets defined 50.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.553A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.582A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 146 through 167 removed outlier: 3.849A pdb=" N GLU A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.707A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.772A pdb=" N LYS A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.055A pdb=" N ILE A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.839A pdb=" N TYR A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 409 through 427 Processing helix chain 'A' and resid 430 through 452 removed outlier: 3.791A pdb=" N LEU A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 569 through 588 removed outlier: 3.566A pdb=" N THR A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 617 through 634 removed outlier: 5.163A pdb=" N ARG A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 666 through 677 removed outlier: 3.634A pdb=" N LEU A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 700 removed outlier: 3.720A pdb=" N LYS A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.791A pdb=" N MET B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 removed outlier: 4.501A pdb=" N SER B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 86 through 102 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.930A pdb=" N HIS B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.718A pdb=" N ASP B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.785A pdb=" N LEU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 removed outlier: 4.129A pdb=" N LYS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.626A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.672A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 4.253A pdb=" N ALA B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.038A pdb=" N THR B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 425 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.627A pdb=" N TRP B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 519 through 538 removed outlier: 4.044A pdb=" N PHE B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.560A pdb=" N LYS B 582 " --> pdb=" O ASN B 578 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.881A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 676 through 696 removed outlier: 3.529A pdb=" N GLU B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 728 Processing helix chain 'B' and resid 732 through 754 removed outlier: 3.725A pdb=" N ARG B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.685A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 removed outlier: 3.537A pdb=" N SER C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER C 57 " --> pdb=" O TRP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.955A pdb=" N ASN C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.794A pdb=" N VAL C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.701A pdb=" N LYS C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 306 through 313 Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 402 through 417 Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.978A pdb=" N LYS C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 4.148A pdb=" N SER C 436 " --> pdb=" O MET C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.613A pdb=" N SER C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 467 removed outlier: 3.638A pdb=" N LEU C 460 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.889A pdb=" N ASP C 535 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 536 " --> pdb=" O ILE C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 536' Processing helix chain 'C' and resid 558 through 573 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 590 through 595 removed outlier: 4.018A pdb=" N LEU C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 595' Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 611 through 630 removed outlier: 3.771A pdb=" N SER C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 641 Processing helix chain 'C' and resid 642 through 644 No H-bonds generated for 'chain 'C' and resid 642 through 644' Processing helix chain 'C' and resid 705 through 709 removed outlier: 3.923A pdb=" N LEU C 708 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 732 Processing helix chain 'C' and resid 758 through 771 removed outlier: 3.878A pdb=" N ASP C 762 " --> pdb=" O ALA C 758 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 771 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 removed outlier: 3.522A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.745A pdb=" N ALA B 454 " --> pdb=" O PHE B 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.643A pdb=" N PHE A 271 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE A 485 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 509 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 506 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 551 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 removed outlier: 4.478A pdb=" N ILE A 456 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 457 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 490 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ALA A 463 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU A 484 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER A 465 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP A 482 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE A 485 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 509 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 556 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.504A pdb=" N GLU B 367 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 369 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 611 through 616 removed outlier: 3.679A pdb=" N GLY A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN A 615 " --> pdb=" O TRP A 604 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP A 604 " --> pdb=" O GLN A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.692A pdb=" N ARG B 138 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.634A pdb=" N ILE B 214 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AB4, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 142 removed outlier: 6.547A pdb=" N TRP C 137 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN C 252 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU C 139 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 153 Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 336 removed outlier: 3.545A pdb=" N LEU C 335 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 342 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU C 374 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 397 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 395 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR C 497 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 396 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 352 through 357 Processing sheet with id=AC1, first strand: chain 'C' and resid 469 through 471 Processing sheet with id=AC2, first strand: chain 'C' and resid 657 through 658 Processing sheet with id=AC3, first strand: chain 'C' and resid 684 through 685 Processing sheet with id=AC4, first strand: chain 'C' and resid 713 through 714 795 hydrogen bonds defined for protein. 2244 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: 13.47 Time building geometry restraints manager: 29.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 17369 1.00 - 1.20: 61 1.20 - 1.40: 7105 1.40 - 1.61: 10566 1.61 - 1.81: 234 Bond restraints: 35335 Sorted by residual: bond pdb=" N3 UIN 44 " pdb=" H3 UIN 44 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" N3 UIN 43 " pdb=" H3 UIN 43 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" C6 UIN 43 " pdb=" H6 UIN 43 " ideal model delta sigma weight residual 0.930 1.085 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" C5 UIN 44 " pdb=" H5 UIN 44 " ideal model delta sigma weight residual 0.930 1.084 -0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" C5 UIN 43 " pdb=" H5 UIN 43 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 35330 not shown) Histogram of bond angle deviations from ideal: 95.45 - 105.56: 458 105.56 - 115.67: 45676 115.67 - 125.77: 17439 125.77 - 135.88: 404 135.88 - 145.99: 3 Bond angle restraints: 63980 Sorted by residual: angle pdb=" CD GLN A 43 " pdb=" NE2 GLN A 43 " pdb="HE22 GLN A 43 " ideal model delta sigma weight residual 120.00 145.99 -25.99 3.00e+00 1.11e-01 7.51e+01 angle pdb="HE21 GLN A 43 " pdb=" NE2 GLN A 43 " pdb="HE22 GLN A 43 " ideal model delta sigma weight residual 120.00 95.45 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb="HE21 GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 95.94 24.06 3.00e+00 1.11e-01 6.43e+01 angle pdb=" CD GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 143.98 -23.98 3.00e+00 1.11e-01 6.39e+01 angle pdb=" CD GLN A 43 " pdb=" NE2 GLN A 43 " pdb="HE21 GLN A 43 " ideal model delta sigma weight residual 120.00 97.77 22.23 3.00e+00 1.11e-01 5.49e+01 ... (remaining 63975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 15709 35.98 - 71.96: 771 71.96 - 107.94: 49 107.94 - 143.93: 2 143.93 - 179.91: 4 Dihedral angle restraints: 16535 sinusoidal: 9298 harmonic: 7237 Sorted by residual: dihedral pdb=" O4' UIN 44 " pdb=" C1' UIN 44 " pdb=" N1 UIN 44 " pdb=" C2 UIN 44 " ideal model delta sinusoidal sigma weight residual -160.00 14.88 -174.88 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' UIN 42 " pdb=" C1' UIN 42 " pdb=" N1 UIN 42 " pdb=" C2 UIN 42 " ideal model delta sinusoidal sigma weight residual -128.00 12.79 -140.79 1 1.70e+01 3.46e-03 5.90e+01 dihedral pdb=" C3' GIN 14 " pdb=" C4' GIN 14 " pdb=" O4' GIN 14 " pdb=" C1' GIN 14 " ideal model delta sinusoidal sigma weight residual 20.00 -10.28 30.28 1 8.00e+00 1.56e-02 2.05e+01 ... (remaining 16532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1909 0.042 - 0.084: 592 0.084 - 0.127: 153 0.127 - 0.169: 13 0.169 - 0.211: 4 Chirality restraints: 2671 Sorted by residual: chirality pdb=" C2' UIN 44 " pdb=" C3' UIN 44 " pdb=" O2' UIN 44 " pdb=" C1' UIN 44 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB THR A 553 " pdb=" CA THR A 553 " pdb=" OG1 THR A 553 " pdb=" CG2 THR A 553 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ARG B 573 " pdb=" N ARG B 573 " pdb=" C ARG B 573 " pdb=" CB ARG B 573 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 2668 not shown) Planarity restraints: 5072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 318 " 0.064 2.00e-02 2.50e+03 9.67e-02 1.40e+02 pdb=" CG ASN A 318 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 318 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 318 " -0.162 2.00e-02 2.50e+03 pdb="HD21 ASN A 318 " -0.031 2.00e-02 2.50e+03 pdb="HD22 ASN A 318 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 672 " 0.068 2.00e-02 2.50e+03 9.50e-02 1.35e+02 pdb=" CG ASN C 672 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 672 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 672 " -0.155 2.00e-02 2.50e+03 pdb="HD21 ASN C 672 " -0.024 2.00e-02 2.50e+03 pdb="HD22 ASN C 672 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 130 " -0.052 2.00e-02 2.50e+03 9.32e-02 1.30e+02 pdb=" CD GLN B 130 " 0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN B 130 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN B 130 " 0.158 2.00e-02 2.50e+03 pdb="HE21 GLN B 130 " 0.041 2.00e-02 2.50e+03 pdb="HE22 GLN B 130 " -0.151 2.00e-02 2.50e+03 ... (remaining 5069 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 3416 2.21 - 2.81: 72862 2.81 - 3.40: 91606 3.40 - 4.00: 121263 4.00 - 4.60: 190528 Nonbonded interactions: 479675 Sorted by model distance: nonbonded pdb=" O CYS A 80 " pdb=" H LEU A 85 " model vdw 1.612 1.850 nonbonded pdb=" O PHE A 48 " pdb="HE21 GLN A 149 " model vdw 1.612 1.850 nonbonded pdb=" HZ3 LYS C 75 " pdb=" OD1 ASP C 85 " model vdw 1.620 1.850 nonbonded pdb=" OE1 GLU A 86 " pdb=" H GLU A 86 " model vdw 1.626 1.850 nonbonded pdb="HD21 ASN A 383 " pdb=" O MET B 1 " model vdw 1.650 1.850 ... (remaining 479670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.180 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: 0.530 Extract box with map and model: 21.110 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 108.910 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.006 0.059 17905 Z= 0.401 Angle : 0.683 6.061 24163 Z= 0.393 Chirality : 0.043 0.211 2671 Planarity : 0.006 0.056 3016 Dihedral : 16.933 174.881 6999 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.17 % Allowed : 14.41 % Favored : 83.42 % 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: -1.90 (0.17), residues: 2113 helix: 0.37 (0.16), residues: 963 sheet: -3.22 (0.32), residues: 210 loop : -2.58 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 53 HIS 0.011 0.002 HIS B 660 PHE 0.030 0.003 PHE B 632 TYR 0.023 0.002 TYR B 6 ARG 0.011 0.001 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 410 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7038 (m-10) cc_final: 0.6334 (m-10) REVERT: A 96 ASP cc_start: 0.7431 (t0) cc_final: 0.6915 (t0) REVERT: A 411 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7493 (tp) REVERT: B 24 TYR cc_start: 0.7942 (m-10) cc_final: 0.7463 (m-10) REVERT: B 133 ASP cc_start: 0.7439 (t0) cc_final: 0.7206 (t0) REVERT: B 519 ASN cc_start: 0.7030 (p0) cc_final: 0.6692 (p0) REVERT: C 58 LYS cc_start: 0.4763 (OUTLIER) cc_final: 0.4413 (mppt) REVERT: C 383 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7081 (p) REVERT: C 481 MET cc_start: 0.7211 (ttt) cc_final: 0.6540 (ttm) REVERT: C 677 SER cc_start: 0.7550 (OUTLIER) cc_final: 0.6869 (t) REVERT: C 718 ASP cc_start: 0.7479 (t0) cc_final: 0.6468 (p0) outliers start: 41 outliers final: 14 residues processed: 441 average time/residue: 0.8567 time to fit residues: 532.4999 Evaluate side-chains 252 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 234 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 677 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 167 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 319 GLN A 529 HIS A 561 ASN A 615 GLN B 62 ASN B 355 GLN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 202 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17905 Z= 0.242 Angle : 0.575 7.060 24163 Z= 0.312 Chirality : 0.039 0.154 2671 Planarity : 0.004 0.056 3016 Dihedral : 10.976 173.243 2626 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.48 % Allowed : 17.27 % Favored : 81.25 % 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: -0.96 (0.18), residues: 2113 helix: 0.99 (0.17), residues: 976 sheet: -2.08 (0.34), residues: 218 loop : -2.11 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 311 HIS 0.010 0.001 HIS A 494 PHE 0.017 0.002 PHE B 556 TYR 0.012 0.001 TYR A 634 ARG 0.005 0.001 ARG B 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 245 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6960 (t0) cc_final: 0.6713 (t0) REVERT: A 52 TYR cc_start: 0.6630 (m-10) cc_final: 0.5950 (m-10) REVERT: A 329 MET cc_start: 0.6871 (mtm) cc_final: 0.6508 (mtp) REVERT: B 41 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7544 (tt0) REVERT: B 96 MET cc_start: 0.8468 (mtt) cc_final: 0.8136 (mtt) REVERT: B 678 MET cc_start: 0.5007 (mpp) cc_final: 0.4757 (mmm) REVERT: C 481 MET cc_start: 0.7193 (ttt) cc_final: 0.6614 (ttm) REVERT: C 718 ASP cc_start: 0.7319 (t0) cc_final: 0.6274 (p0) outliers start: 28 outliers final: 17 residues processed: 269 average time/residue: 0.7736 time to fit residues: 299.4872 Evaluate side-chains 229 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 675 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 0.0870 chunk 132 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 702 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17905 Z= 0.211 Angle : 0.513 5.852 24163 Z= 0.276 Chirality : 0.037 0.153 2671 Planarity : 0.004 0.064 3016 Dihedral : 10.707 179.083 2612 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.75 % Allowed : 17.27 % Favored : 80.99 % 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: -0.53 (0.18), residues: 2113 helix: 1.26 (0.17), residues: 981 sheet: -1.74 (0.36), residues: 208 loop : -1.84 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 53 HIS 0.005 0.001 HIS A 494 PHE 0.013 0.001 PHE B 556 TYR 0.011 0.001 TYR B 6 ARG 0.006 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7471 (tp30) cc_final: 0.7257 (tp30) REVERT: A 52 TYR cc_start: 0.6633 (m-10) cc_final: 0.5880 (m-10) REVERT: A 329 MET cc_start: 0.6897 (mtm) cc_final: 0.6562 (mtp) REVERT: B 41 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7763 (tt0) REVERT: B 96 MET cc_start: 0.8410 (mtt) cc_final: 0.8071 (mtt) REVERT: C 481 MET cc_start: 0.7235 (ttt) cc_final: 0.6577 (ttm) REVERT: C 718 ASP cc_start: 0.7346 (t0) cc_final: 0.6457 (p0) outliers start: 33 outliers final: 21 residues processed: 239 average time/residue: 0.7378 time to fit residues: 260.6158 Evaluate side-chains 222 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 675 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 195 optimal weight: 0.0970 chunk 206 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 644 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17905 Z= 0.161 Angle : 0.479 5.698 24163 Z= 0.254 Chirality : 0.037 0.154 2671 Planarity : 0.003 0.043 3016 Dihedral : 10.484 171.804 2610 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.38 % Allowed : 17.64 % Favored : 80.99 % 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 (0.19), residues: 2113 helix: 1.46 (0.17), residues: 987 sheet: -1.58 (0.36), residues: 211 loop : -1.65 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 53 HIS 0.007 0.001 HIS A 494 PHE 0.010 0.001 PHE C 658 TYR 0.008 0.001 TYR B 6 ARG 0.004 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7452 (tp30) cc_final: 0.7237 (tp30) REVERT: A 329 MET cc_start: 0.6877 (mtm) cc_final: 0.6468 (mtp) REVERT: A 562 ASP cc_start: 0.8037 (t70) cc_final: 0.7749 (t0) REVERT: B 172 MET cc_start: 0.8574 (mmm) cc_final: 0.7630 (mmt) REVERT: B 243 ILE cc_start: 0.8226 (tt) cc_final: 0.7942 (mt) REVERT: B 496 MET cc_start: 0.5950 (ttp) cc_final: 0.5745 (ttm) REVERT: C 718 ASP cc_start: 0.7323 (t0) cc_final: 0.6466 (p0) outliers start: 26 outliers final: 22 residues processed: 227 average time/residue: 0.7199 time to fit residues: 244.4029 Evaluate side-chains 213 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17905 Z= 0.234 Angle : 0.515 6.214 24163 Z= 0.276 Chirality : 0.038 0.154 2671 Planarity : 0.003 0.046 3016 Dihedral : 10.394 161.508 2608 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.91 % Allowed : 17.37 % Favored : 80.72 % 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: -0.27 (0.18), residues: 2113 helix: 1.41 (0.17), residues: 979 sheet: -1.37 (0.37), residues: 201 loop : -1.68 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 172 HIS 0.008 0.001 HIS A 494 PHE 0.015 0.001 PHE B 556 TYR 0.014 0.001 TYR C 447 ARG 0.003 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7631 (tp30) cc_final: 0.7384 (tp30) REVERT: A 52 TYR cc_start: 0.6381 (m-10) cc_final: 0.6180 (m-10) REVERT: A 329 MET cc_start: 0.6889 (mtm) cc_final: 0.6536 (mtp) REVERT: A 575 MET cc_start: 0.8220 (tpp) cc_final: 0.7461 (tpt) REVERT: B 175 MET cc_start: 0.9076 (mtp) cc_final: 0.8860 (mtp) REVERT: C 481 MET cc_start: 0.7077 (ttt) cc_final: 0.6504 (ttm) REVERT: C 664 PHE cc_start: 0.8821 (p90) cc_final: 0.8496 (p90) REVERT: C 718 ASP cc_start: 0.7315 (t0) cc_final: 0.6496 (p0) outliers start: 36 outliers final: 27 residues processed: 229 average time/residue: 0.6657 time to fit residues: 234.2191 Evaluate side-chains 219 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.0040 chunk 186 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 68 optimal weight: 0.0970 chunk 108 optimal weight: 0.6980 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN B 108 HIS ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17905 Z= 0.130 Angle : 0.453 4.820 24163 Z= 0.239 Chirality : 0.036 0.154 2671 Planarity : 0.003 0.046 3016 Dihedral : 10.223 161.468 2608 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.54 % Allowed : 17.64 % Favored : 80.83 % 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: 0.08 (0.19), residues: 2113 helix: 1.77 (0.17), residues: 976 sheet: -1.28 (0.37), residues: 212 loop : -1.55 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 53 HIS 0.006 0.001 HIS A 494 PHE 0.020 0.001 PHE A 706 TYR 0.007 0.001 TYR A 634 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7610 (tp30) cc_final: 0.7390 (tp30) REVERT: A 50 ASP cc_start: 0.7219 (t0) cc_final: 0.6903 (t0) REVERT: A 52 TYR cc_start: 0.6395 (m-10) cc_final: 0.5937 (m-10) REVERT: A 329 MET cc_start: 0.6850 (mtm) cc_final: 0.6437 (mtp) REVERT: B 528 MET cc_start: 0.8202 (mtm) cc_final: 0.7998 (mtm) REVERT: C 481 MET cc_start: 0.7129 (ttt) cc_final: 0.6462 (ttm) REVERT: C 718 ASP cc_start: 0.7284 (t0) cc_final: 0.6435 (p0) outliers start: 29 outliers final: 23 residues processed: 218 average time/residue: 0.6704 time to fit residues: 220.5076 Evaluate side-chains 212 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 529 HIS Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 151 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 0.0010 chunk 206 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 0.1980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17905 Z= 0.170 Angle : 0.461 4.648 24163 Z= 0.244 Chirality : 0.036 0.152 2671 Planarity : 0.003 0.046 3016 Dihedral : 10.080 160.494 2605 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.54 % Allowed : 17.90 % Favored : 80.56 % 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: 0.11 (0.19), residues: 2113 helix: 1.77 (0.17), residues: 979 sheet: -1.15 (0.36), residues: 213 loop : -1.56 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 53 HIS 0.010 0.001 HIS A 529 PHE 0.010 0.001 PHE B 556 TYR 0.009 0.001 TYR C 447 ARG 0.004 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7633 (tp30) cc_final: 0.7415 (tp30) REVERT: A 50 ASP cc_start: 0.7248 (t0) cc_final: 0.6968 (t0) REVERT: A 52 TYR cc_start: 0.6363 (m-10) cc_final: 0.5885 (m-10) REVERT: A 329 MET cc_start: 0.6898 (mtm) cc_final: 0.6490 (mtp) REVERT: A 494 HIS cc_start: 0.7213 (m-70) cc_final: 0.6897 (m170) REVERT: C 481 MET cc_start: 0.7178 (ttt) cc_final: 0.6477 (ttm) REVERT: C 718 ASP cc_start: 0.7302 (t0) cc_final: 0.6442 (p0) outliers start: 29 outliers final: 25 residues processed: 218 average time/residue: 0.6813 time to fit residues: 226.1538 Evaluate side-chains 218 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN B 84 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17905 Z= 0.250 Angle : 0.505 4.884 24163 Z= 0.272 Chirality : 0.037 0.154 2671 Planarity : 0.003 0.048 3016 Dihedral : 10.123 159.249 2605 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.69 % Allowed : 18.06 % Favored : 80.24 % 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: -0.08 (0.18), residues: 2113 helix: 1.56 (0.17), residues: 975 sheet: -1.16 (0.37), residues: 213 loop : -1.59 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 439 HIS 0.007 0.001 HIS A 494 PHE 0.025 0.002 PHE A 706 TYR 0.014 0.001 TYR C 447 ARG 0.007 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7621 (tp30) cc_final: 0.7400 (tp30) REVERT: A 329 MET cc_start: 0.6902 (mtm) cc_final: 0.6564 (mtp) REVERT: A 494 HIS cc_start: 0.7241 (m-70) cc_final: 0.6922 (m170) REVERT: B 679 MET cc_start: 0.6057 (tmm) cc_final: 0.5535 (tpp) REVERT: C 378 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6632 (tm-30) REVERT: C 481 MET cc_start: 0.7198 (ttt) cc_final: 0.6493 (ttm) REVERT: C 718 ASP cc_start: 0.7386 (t0) cc_final: 0.6782 (p0) outliers start: 32 outliers final: 29 residues processed: 225 average time/residue: 0.7461 time to fit residues: 249.8376 Evaluate side-chains 222 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17905 Z= 0.173 Angle : 0.473 5.670 24163 Z= 0.251 Chirality : 0.037 0.153 2671 Planarity : 0.003 0.048 3016 Dihedral : 10.025 159.282 2603 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.48 % Allowed : 18.54 % Favored : 79.98 % 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: 0.06 (0.19), residues: 2113 helix: 1.69 (0.17), residues: 979 sheet: -1.08 (0.37), residues: 213 loop : -1.56 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 53 HIS 0.007 0.001 HIS A 494 PHE 0.013 0.001 PHE A 706 TYR 0.008 0.001 TYR C 447 ARG 0.005 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7723 (tp30) cc_final: 0.7480 (tp30) REVERT: A 329 MET cc_start: 0.6896 (mtm) cc_final: 0.6574 (mtp) REVERT: A 575 MET cc_start: 0.8232 (tpp) cc_final: 0.7426 (tpt) REVERT: B 679 MET cc_start: 0.6036 (tmm) cc_final: 0.5512 (tpp) REVERT: C 481 MET cc_start: 0.7096 (ttt) cc_final: 0.6486 (ttm) REVERT: C 718 ASP cc_start: 0.7368 (t0) cc_final: 0.6769 (p0) outliers start: 28 outliers final: 26 residues processed: 220 average time/residue: 0.7580 time to fit residues: 245.4983 Evaluate side-chains 216 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 96 optimal weight: 0.0060 chunk 141 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 169 optimal weight: 0.0170 chunk 17 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17905 Z= 0.147 Angle : 0.461 5.687 24163 Z= 0.242 Chirality : 0.036 0.152 2671 Planarity : 0.003 0.049 3016 Dihedral : 9.943 159.385 2603 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.54 % Allowed : 18.49 % Favored : 79.98 % 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: 0.24 (0.19), residues: 2113 helix: 1.86 (0.17), residues: 980 sheet: -0.99 (0.37), residues: 212 loop : -1.50 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 53 HIS 0.006 0.001 HIS A 494 PHE 0.014 0.001 PHE A 706 TYR 0.009 0.001 TYR B 685 ARG 0.004 0.000 ARG C 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7709 (tp30) cc_final: 0.7487 (tp30) REVERT: A 329 MET cc_start: 0.6857 (mtm) cc_final: 0.6545 (mtp) REVERT: B 679 MET cc_start: 0.6134 (tmm) cc_final: 0.5897 (tmm) REVERT: C 481 MET cc_start: 0.7127 (ttt) cc_final: 0.6465 (ttm) REVERT: C 718 ASP cc_start: 0.7334 (t0) cc_final: 0.6735 (p0) outliers start: 29 outliers final: 25 residues processed: 214 average time/residue: 0.7093 time to fit residues: 225.7055 Evaluate side-chains 216 residues out of total 1888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 156 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 174 optimal weight: 0.4980 chunk 21 optimal weight: 0.0060 chunk 31 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 HIS A 609 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.114890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097073 restraints weight = 105701.827| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.94 r_work: 0.3418 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17905 Z= 0.157 Angle : 0.467 6.430 24163 Z= 0.247 Chirality : 0.036 0.151 2671 Planarity : 0.003 0.050 3016 Dihedral : 9.906 159.207 2603 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.48 % Allowed : 18.64 % Favored : 79.87 % 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: 0.27 (0.19), residues: 2113 helix: 1.88 (0.17), residues: 980 sheet: -0.98 (0.37), residues: 212 loop : -1.47 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 53 HIS 0.007 0.001 HIS A 494 PHE 0.042 0.001 PHE A 90 TYR 0.008 0.001 TYR C 447 ARG 0.004 0.000 ARG B 568 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7858.77 seconds wall clock time: 140 minutes 38.19 seconds (8438.19 seconds total)