Starting phenix.real_space_refine (version: dev) on Wed Dec 14 08:05:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwg_21934/12_2022/6wwg_21934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwg_21934/12_2022/6wwg_21934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwg_21934/12_2022/6wwg_21934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwg_21934/12_2022/6wwg_21934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwg_21934/12_2022/6wwg_21934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwg_21934/12_2022/6wwg_21934_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "K PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 447": "OE1" <-> "OE2" Residue "K GLU 460": "OE1" <-> "OE2" Residue "K PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 520": "OE1" <-> "OE2" Residue "K TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 539": "OD1" <-> "OD2" Residue "K TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 683": "NH1" <-> "NH2" Residue "K PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 744": "OE1" <-> "OE2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "N PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 406": "NH1" <-> "NH2" Residue "N PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 497": "OE1" <-> "OE2" Residue "N PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 604": "NH1" <-> "NH2" Residue "N GLU 643": "OE1" <-> "OE2" Residue "N ARG 644": "NH1" <-> "NH2" Residue "N TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 33": "OD1" <-> "OD2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 424": "OD1" <-> "OD2" Residue "I ASP 26": "OD1" <-> "OD2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 19749 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2880 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain: "B" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3411 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain: "N" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2860 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain: "E" Number of atoms: 3458 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Conformer: "B" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} bond proxies already assigned to first conformer: 3510 Chain: "I" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3389 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR E 108 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 108 " occ=0.50 Time building chain proxies: 13.33, per 1000 atoms: 0.67 Number of scatterers: 19749 At special positions: 0 Unit cell: (110.684, 71.862, 192.458, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 126 16.00 P 14 15.00 Al 1 13.00 Mg 3 11.99 F 3 9.00 O 3860 8.00 N 3363 7.00 C 12379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.46 Conformation dependent library (CDL) restraints added in 3.3 seconds 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4606 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 20 sheets defined 40.1% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'K' and resid 405 through 409 Processing helix chain 'K' and resid 455 through 472 removed outlier: 4.769A pdb=" N ALA K 464 " --> pdb=" O GLU K 460 " (cutoff:3.500A) Proline residue: K 465 - end of helix Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 501 through 515 Processing helix chain 'K' and resid 577 through 590 Processing helix chain 'K' and resid 653 through 675 Processing helix chain 'K' and resid 692 through 701 removed outlier: 5.482A pdb=" N GLU K 699 " --> pdb=" O TRP K 695 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER K 700 " --> pdb=" O LEU K 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 720 through 735 removed outlier: 4.176A pdb=" N LEU K 735 " --> pdb=" O THR K 731 " (cutoff:3.500A) Processing helix chain 'K' and resid 751 through 754 No H-bonds generated for 'chain 'K' and resid 751 through 754' Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.890A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.986A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.698A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.488A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.505A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.742A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.848A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.920A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.613A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.549A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.557A pdb=" N LYS A 394 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.703A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.677A pdb=" N GLU A 420 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 423 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 432 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 435 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.680A pdb=" N GLN B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.537A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 125 removed outlier: 4.841A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.688A pdb=" N LEU B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.538A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 235 removed outlier: 4.257A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.622A pdb=" N GLN B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.690A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 372 through 389 removed outlier: 3.709A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 4.164A pdb=" N THR B 399 " --> pdb=" O HIS B 396 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY B 400 " --> pdb=" O TRP B 397 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 401 " --> pdb=" O TYR B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 426 removed outlier: 3.789A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 412 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 409 Processing helix chain 'N' and resid 455 through 462 Processing helix chain 'N' and resid 464 through 470 Processing helix chain 'N' and resid 488 through 492 Processing helix chain 'N' and resid 501 through 516 Processing helix chain 'N' and resid 577 through 590 removed outlier: 3.884A pdb=" N TRP N 583 " --> pdb=" O ASP N 579 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS N 589 " --> pdb=" O GLU N 585 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN N 590 " --> pdb=" O LEU N 586 " (cutoff:3.500A) Processing helix chain 'N' and resid 655 through 679 removed outlier: 3.920A pdb=" N VAL N 659 " --> pdb=" O LEU N 655 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER N 660 " --> pdb=" O LYS N 656 " (cutoff:3.500A) Processing helix chain 'N' and resid 692 through 696 Processing helix chain 'N' and resid 699 through 701 No H-bonds generated for 'chain 'N' and resid 699 through 701' Processing helix chain 'N' and resid 717 through 728 removed outlier: 3.821A pdb=" N ILE N 720 " --> pdb=" O ALA N 717 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLU N 721 " --> pdb=" O SER N 718 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU N 724 " --> pdb=" O GLU N 721 " (cutoff:3.500A) Processing helix chain 'N' and resid 750 through 754 Processing helix chain 'E' and resid 10 through 28 removed outlier: 3.796A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS E 25 " --> pdb=" O TRP E 21 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 Processing helix chain 'E' and resid 72 through 79 removed outlier: 4.054A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 109 through 111 No H-bonds generated for 'chain 'E' and resid 109 through 111' Processing helix chain 'E' and resid 117 through 128 removed outlier: 4.206A pdb=" N ARG E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 160 removed outlier: 3.526A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 removed outlier: 3.703A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 238 removed outlier: 4.055A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.756A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 281 No H-bonds generated for 'chain 'E' and resid 278 through 281' Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.828A pdb=" N ASN E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 399 removed outlier: 3.651A pdb=" N LYS E 394 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET E 398 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.835A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 423 removed outlier: 3.662A pdb=" N SER E 419 " --> pdb=" O GLY E 416 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU E 420 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 421 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG E 422 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU E 423 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 436 removed outlier: 3.874A pdb=" N GLU E 429 " --> pdb=" O MET E 425 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS E 430 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY E 436 " --> pdb=" O TYR E 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 removed outlier: 3.929A pdb=" N LYS I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 45 No H-bonds generated for 'chain 'I' and resid 42 through 45' Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 71 through 77 Processing helix chain 'I' and resid 82 through 84 No H-bonds generated for 'chain 'I' and resid 82 through 84' Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 125 removed outlier: 4.817A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 158 Processing helix chain 'I' and resid 179 through 195 Proline residue: I 182 - end of helix removed outlier: 4.395A pdb=" N VAL I 193 " --> pdb=" O HIS I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 222 through 240 removed outlier: 3.837A pdb=" N ALA I 231 " --> pdb=" O HIS I 227 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N CYS I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 Processing helix chain 'I' and resid 286 through 294 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 305 through 307 No H-bonds generated for 'chain 'I' and resid 305 through 307' Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 372 through 389 removed outlier: 3.548A pdb=" N GLN I 384 " --> pdb=" O ILE I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 399 No H-bonds generated for 'chain 'I' and resid 396 through 399' Processing helix chain 'I' and resid 405 through 422 Processing sheet with id= A, first strand: chain 'K' and resid 440 through 443 removed outlier: 3.588A pdb=" N VAL K 440 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU K 525 " --> pdb=" O VAL K 574 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 416 through 418 Processing sheet with id= C, first strand: chain 'K' and resid 530 through 533 Processing sheet with id= D, first strand: chain 'K' and resid 555 through 559 removed outlier: 3.914A pdb=" N ARG K 555 " --> pdb=" O GLU K 567 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.502A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'A' and resid 351 through 356 removed outlier: 8.547A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.102A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS B 129 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N VAL B 5 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLN B 131 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 13.147A pdb=" N ILE B 7 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N PHE B 133 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 12.451A pdb=" N ALA B 9 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU B 135 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= J, first strand: chain 'B' and resid 269 through 271 removed outlier: 3.613A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 440 through 443 removed outlier: 3.794A pdb=" N VAL N 440 " --> pdb=" O VAL N 396 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET N 709 " --> pdb=" O THR N 395 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN N 475 " --> pdb=" O LYS N 706 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA N 708 " --> pdb=" O ASN N 475 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS N 477 " --> pdb=" O ALA N 708 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE N 710 " --> pdb=" O CYS N 477 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE N 479 " --> pdb=" O ILE N 710 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR N 712 " --> pdb=" O PHE N 479 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR N 481 " --> pdb=" O THR N 712 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N SER N 714 " --> pdb=" O TYR N 481 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS N 628 " --> pdb=" O LYS N 617 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU N 525 " --> pdb=" O VAL N 574 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 424 through 426 Processing sheet with id= M, first strand: chain 'N' and resid 530 through 533 Processing sheet with id= N, first strand: chain 'N' and resid 555 through 559 removed outlier: 4.564A pdb=" N ARG N 555 " --> pdb=" O GLU N 567 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 65 through 68 removed outlier: 8.388A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE E 5 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE E 135 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE E 7 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL E 137 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL E 9 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS E 139 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= Q, first strand: chain 'E' and resid 269 through 272 removed outlier: 3.518A pdb=" N MET E 377 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS E 352 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR E 319 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY E 354 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY E 321 " --> pdb=" O GLY E 354 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 90 through 92 removed outlier: 7.850A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS I 129 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL I 5 " --> pdb=" O CYS I 129 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N GLN I 131 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 12.616A pdb=" N ILE I 7 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N PHE I 133 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 11.953A pdb=" N ALA I 9 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N LEU I 135 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE I 163 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU I 135 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN I 165 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N HIS I 137 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE I 167 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU I 198 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER I 168 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR I 200 " --> pdb=" O SER I 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 51 through 53 Processing sheet with id= T, first strand: chain 'I' and resid 269 through 271 677 hydrogen bonds defined for protein. 1722 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: 6.31 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3841 1.32 - 1.45: 4973 1.45 - 1.57: 11139 1.57 - 1.69: 22 1.69 - 1.81: 205 Bond restraints: 20180 Sorted by residual: bond pdb=" C27 TA1 I 502 " pdb=" O11 TA1 I 502 " ideal model delta sigma weight residual 1.329 1.451 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C22 TA1 I 502 " pdb=" O09 TA1 I 502 " ideal model delta sigma weight residual 1.335 1.456 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C27 TA1 B 502 " pdb=" O11 TA1 B 502 " ideal model delta sigma weight residual 1.329 1.449 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C22 TA1 B 502 " pdb=" O09 TA1 B 502 " ideal model delta sigma weight residual 1.335 1.454 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C12 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 1.337 1.449 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 20175 not shown) Histogram of bond angle deviations from ideal: 87.61 - 97.34: 8 97.34 - 107.07: 682 107.07 - 116.81: 13328 116.81 - 126.54: 13112 126.54 - 136.28: 271 Bond angle restraints: 27401 Sorted by residual: angle pdb=" C PRO I 357 " pdb=" N PRO I 358 " pdb=" CA PRO I 358 " ideal model delta sigma weight residual 119.78 126.27 -6.49 1.03e+00 9.43e-01 3.97e+01 angle pdb=" C ALA E 427 " pdb=" N LEU E 428 " pdb=" CA LEU E 428 " ideal model delta sigma weight residual 120.28 129.17 -8.89 1.44e+00 4.82e-01 3.81e+01 angle pdb=" C PRO B 357 " pdb=" N PRO B 358 " pdb=" CA PRO B 358 " ideal model delta sigma weight residual 119.85 125.37 -5.52 1.01e+00 9.80e-01 2.99e+01 angle pdb=" CA BTYR E 108 " pdb=" C BTYR E 108 " pdb=" O BTYR E 108 " ideal model delta sigma weight residual 120.51 113.29 7.22 1.43e+00 4.89e-01 2.55e+01 angle pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" C GLU B 22 " ideal model delta sigma weight residual 112.89 106.73 6.16 1.24e+00 6.50e-01 2.46e+01 ... (remaining 27396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 11707 33.79 - 67.59: 260 67.59 - 101.38: 26 101.38 - 135.17: 3 135.17 - 168.97: 3 Dihedral angle restraints: 11999 sinusoidal: 4823 harmonic: 7176 Sorted by residual: dihedral pdb=" CD ARG B 359 " pdb=" NE ARG B 359 " pdb=" CZ ARG B 359 " pdb=" NH1 ARG B 359 " ideal model delta sinusoidal sigma weight residual 0.00 80.47 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CD ARG N 654 " pdb=" NE ARG N 654 " pdb=" CZ ARG N 654 " pdb=" NH1 ARG N 654 " ideal model delta sinusoidal sigma weight residual 0.00 -69.70 69.70 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 291.08 122.11 168.97 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 11996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2724 0.094 - 0.188: 253 0.188 - 0.282: 36 0.282 - 0.375: 2 0.375 - 0.469: 2 Chirality restraints: 3017 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.69 -0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C18 TA1 I 502 " pdb=" C10 TA1 I 502 " pdb=" C17 TA1 I 502 " pdb=" C20 TA1 I 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.70 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA THR E 109 " pdb=" N THR E 109 " pdb=" C THR E 109 " pdb=" CB THR E 109 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 3014 not shown) Planarity restraints: 3544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 359 " -1.082 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG B 359 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 359 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 359 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 359 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 654 " -1.030 9.50e-02 1.11e+02 4.62e-01 1.29e+02 pdb=" NE ARG N 654 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG N 654 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG N 654 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG N 654 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 TA1 B 502 " -0.119 2.00e-02 2.50e+03 9.51e-02 1.13e+02 pdb=" C30 TA1 B 502 " 0.029 2.00e-02 2.50e+03 pdb=" C31 TA1 B 502 " -0.088 2.00e-02 2.50e+03 pdb=" N01 TA1 B 502 " 0.147 2.00e-02 2.50e+03 pdb=" O14 TA1 B 502 " 0.031 2.00e-02 2.50e+03 ... (remaining 3541 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 143 2.56 - 3.14: 15624 3.14 - 3.73: 29512 3.73 - 4.31: 44002 4.31 - 4.90: 73714 Nonbonded interactions: 162995 Sorted by model distance: nonbonded pdb=" O3G GTP E 501 " pdb="MG MG E 502 " model vdw 1.969 2.170 nonbonded pdb=" OG SER K 489 " pdb="MG MG K 802 " model vdw 2.012 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.012 2.170 nonbonded pdb=" O2B ADP K 801 " pdb="MG MG K 802 " model vdw 2.025 2.170 nonbonded pdb=" O ASN A 186 " pdb=" OG1 THR A 190 " model vdw 2.026 2.440 ... (remaining 162990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 109 through 441 or resid 501 throug \ h 502)) selection = (chain 'E' and (resid 1 through 107 or resid 109 through 441 or resid 501 throug \ h 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 431 or resid 501 through 502)) selection = chain 'I' } ncs_group { reference = (chain 'K' and resid 391 through 755) selection = (chain 'N' and resid 391 through 755) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 14 5.49 5 Mg 3 5.21 5 S 126 5.16 5 C 12379 2.51 5 N 3363 2.21 5 O 3860 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.920 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.190 Process input model: 54.190 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.122 20180 Z= 0.472 Angle : 0.928 12.362 27401 Z= 0.544 Chirality : 0.058 0.469 3017 Planarity : 0.017 0.485 3544 Dihedral : 14.851 168.969 7393 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.66 % Favored : 95.05 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.15), residues: 2470 helix: -2.58 (0.13), residues: 981 sheet: -1.17 (0.24), residues: 434 loop : -2.45 (0.17), residues: 1055 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 589 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 16 residues processed: 632 average time/residue: 1.1022 time to fit residues: 800.8946 Evaluate side-chains 436 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 420 time to evaluate : 2.373 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.2509 time to fit residues: 3.7580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 192 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 534 ASN K 599 ASN A 206 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN A 358 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 195 ASN B 337 ASN B 375 GLN N 590 GLN N 635 ASN N 732 GLN E 8 HIS E 50 ASN E 192 HIS ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 43 GLN I 99 ASN I 131 GLN I 245 GLN I 280 GLN I 298 ASN ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 20180 Z= 0.240 Angle : 0.634 9.299 27401 Z= 0.313 Chirality : 0.045 0.362 3017 Planarity : 0.005 0.050 3544 Dihedral : 9.535 165.095 2778 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2470 helix: -1.09 (0.16), residues: 1002 sheet: -0.42 (0.24), residues: 451 loop : -2.02 (0.18), residues: 1017 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 436 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 34 residues processed: 493 average time/residue: 1.1187 time to fit residues: 634.6590 Evaluate side-chains 431 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 397 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 25 residues processed: 9 average time/residue: 0.6071 time to fit residues: 10.4226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 185 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 599 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 131 GLN B 245 GLN B 247 ASN N 455 GLN ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN I 37 HIS ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN I 280 GLN I 298 ASN I 347 ASN I 375 GLN I 423 GLN I 426 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20180 Z= 0.212 Angle : 0.582 7.361 27401 Z= 0.284 Chirality : 0.044 0.284 3017 Planarity : 0.004 0.041 3544 Dihedral : 9.072 164.413 2778 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.44 (0.17), residues: 2470 helix: -0.51 (0.16), residues: 1002 sheet: -0.08 (0.24), residues: 471 loop : -1.77 (0.19), residues: 997 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 419 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 46 residues processed: 465 average time/residue: 1.1726 time to fit residues: 626.6777 Evaluate side-chains 430 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 384 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 31 residues processed: 17 average time/residue: 0.4802 time to fit residues: 14.0479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 224 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 524 HIS K 588 ASN A 85 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 256 GLN A 358 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN E 128 GLN E 249 ASN E 266 HIS E 300 ASN E 329 ASN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 20180 Z= 0.269 Angle : 0.595 7.144 27401 Z= 0.290 Chirality : 0.045 0.275 3017 Planarity : 0.004 0.040 3544 Dihedral : 8.896 158.036 2778 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.11 (0.17), residues: 2470 helix: -0.15 (0.17), residues: 986 sheet: 0.10 (0.24), residues: 470 loop : -1.67 (0.19), residues: 1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 425 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 48 residues processed: 476 average time/residue: 1.1271 time to fit residues: 614.9861 Evaluate side-chains 441 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 393 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 34 residues processed: 16 average time/residue: 0.5457 time to fit residues: 14.4626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 177 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN B 6 HIS B 8 GLN B 37 HIS B 375 GLN N 732 GLN E 128 GLN E 206 ASN E 300 ASN E 329 ASN I 6 HIS I 8 GLN I 15 GLN I 48 ASN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN I 423 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 20180 Z= 0.437 Angle : 0.657 7.073 27401 Z= 0.323 Chirality : 0.049 0.277 3017 Planarity : 0.004 0.046 3544 Dihedral : 9.141 148.477 2778 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.07 (0.17), residues: 2470 helix: -0.10 (0.17), residues: 985 sheet: 0.14 (0.25), residues: 454 loop : -1.66 (0.18), residues: 1031 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 401 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 60 residues processed: 455 average time/residue: 1.1540 time to fit residues: 605.4017 Evaluate side-chains 452 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 392 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 40 residues processed: 22 average time/residue: 0.4979 time to fit residues: 17.4088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN E 128 GLN ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN I 15 GLN I 48 ASN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN I 245 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 20180 Z= 0.194 Angle : 0.578 7.997 27401 Z= 0.279 Chirality : 0.044 0.271 3017 Planarity : 0.004 0.043 3544 Dihedral : 8.772 147.853 2778 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.72 (0.17), residues: 2470 helix: 0.23 (0.17), residues: 985 sheet: 0.26 (0.25), residues: 458 loop : -1.49 (0.19), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 395 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 49 residues processed: 451 average time/residue: 1.1657 time to fit residues: 606.0341 Evaluate side-chains 422 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 373 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 42 residues processed: 10 average time/residue: 0.6715 time to fit residues: 11.5584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 237 optimal weight: 0.0770 chunk 148 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN N 732 GLN E 128 GLN ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 83 GLN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 20180 Z= 0.177 Angle : 0.570 8.993 27401 Z= 0.274 Chirality : 0.043 0.254 3017 Planarity : 0.004 0.037 3544 Dihedral : 8.553 146.097 2778 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.50 (0.17), residues: 2470 helix: 0.41 (0.17), residues: 981 sheet: 0.40 (0.25), residues: 454 loop : -1.36 (0.19), residues: 1035 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 389 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 56 residues processed: 437 average time/residue: 1.1091 time to fit residues: 564.0078 Evaluate side-chains 425 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 369 time to evaluate : 2.136 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 42 residues processed: 17 average time/residue: 0.2971 time to fit residues: 10.8373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN E 128 GLN E 372 GLN I 11 GLN I 15 GLN I 48 ASN I 83 GLN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN I 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 20180 Z= 0.381 Angle : 0.657 10.966 27401 Z= 0.319 Chirality : 0.047 0.250 3017 Planarity : 0.004 0.041 3544 Dihedral : 8.838 140.752 2778 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.62 (0.17), residues: 2470 helix: 0.33 (0.17), residues: 973 sheet: 0.35 (0.25), residues: 454 loop : -1.43 (0.19), residues: 1043 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 398 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 58 residues processed: 453 average time/residue: 1.0721 time to fit residues: 563.7358 Evaluate side-chains 443 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 385 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 47 residues processed: 13 average time/residue: 0.6002 time to fit residues: 13.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 0.9980 chunk 227 optimal weight: 0.1980 chunk 207 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 208 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN I 15 GLN I 48 ASN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20180 Z= 0.198 Angle : 0.594 11.971 27401 Z= 0.285 Chirality : 0.044 0.252 3017 Planarity : 0.004 0.047 3544 Dihedral : 8.528 138.525 2778 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.47 (0.17), residues: 2470 helix: 0.49 (0.17), residues: 976 sheet: 0.38 (0.25), residues: 454 loop : -1.38 (0.19), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 376 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 51 residues processed: 427 average time/residue: 1.0766 time to fit residues: 532.8161 Evaluate side-chains 416 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 365 time to evaluate : 2.380 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 47 residues processed: 7 average time/residue: 0.2457 time to fit residues: 6.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 0.0970 chunk 245 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 0.0060 chunk 155 optimal weight: 10.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 358 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 48 ASN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20180 Z= 0.183 Angle : 0.591 12.544 27401 Z= 0.283 Chirality : 0.043 0.247 3017 Planarity : 0.004 0.083 3544 Dihedral : 8.340 135.364 2778 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.32 (0.17), residues: 2470 helix: 0.64 (0.17), residues: 972 sheet: 0.40 (0.25), residues: 457 loop : -1.29 (0.19), residues: 1041 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 387 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 51 residues processed: 433 average time/residue: 1.1123 time to fit residues: 561.7840 Evaluate side-chains 421 residues out of total 2127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 370 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 46 residues processed: 7 average time/residue: 0.5335 time to fit residues: 7.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 195 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 48 ASN I 99 ASN ** I 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.129406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102962 restraints weight = 31679.056| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.33 r_work: 0.3339 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3902 r_free = 0.3902 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20180 Z= 0.188 Angle : 0.585 11.557 27401 Z= 0.280 Chirality : 0.044 0.242 3017 Planarity : 0.004 0.068 3544 Dihedral : 8.284 133.275 2778 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.26 (0.17), residues: 2470 helix: 0.65 (0.17), residues: 976 sheet: 0.39 (0.25), residues: 463 loop : -1.21 (0.19), residues: 1031 =============================================================================== Job complete usr+sys time: 9023.78 seconds wall clock time: 160 minutes 12.93 seconds (9612.93 seconds total)